title: Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [TT-seq]

status: Public on Sep 29 2021

city: Shanghai

first: Linna

last: Peng

address: Dong'an Road

country: China

institute: Fudan University

type: Expression profiling by high throughput sequencing

summary: Transcription machinery progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Yet its mechanistic understanding in human cells remains incomplete. Here we utilize rapid degradation system and reveal crucial function of SPT5 in maintaining cellular and chromatin Pol II levels. Rapid SPT5 depletion causes a pronounced reduction of paused Pol II at promoters and enhancers, distinct from NELF degradation resulting in short-distance paused Pol II redistribution. Most of genes exhibit down- but not upregulation, accompanied by greatly impaired transcription activation and altered chromatin landscape at enhancers, and severe Pol II processivity defects at gene bodies. Phosphorylation of KOWx-4/5- linker potentiates pause release and is antagonized by Integrator-PP2A (INTAC) targeting SPT5 and Pol II. Our findings position SPT5 as an essential positive regulator of global transcription by controlling cellular Pol II levels, enhancer activation and landscape, paused Pol II stability, elongation processivity and termination in human.

overall_design: We performed PRO-seq, ATAC-seq, RNA-seq, ChIP-seq, or TT-seq to investigate the role of SPT5 in regulating transcription. In this study, samples for each condition were collected in biological duplicates. Cells were treated with dTAG13 for 3, 12,or 24 hours, the corresponding control cells were treated for the same duration with vehicle only (DMSO) at the same vol/vol dilution.

first: Shibin

last: Hu

first: Zhenning

last: Wang

first: Aixia

last: Song

first: Fei

middle: X

last: Chen


title: The histone acetyltransferase HBO1 (KAT7) promotes efficient tip cell sprouting during angiogenesis

status: Public on Sep 30 2021

city: Parkville

first: Peter

last: Hickey

address: 1G Royal Parade

country: Australia

institute: WEHI

summary: Blood vessel growth and remodelling are essential during embryonic development and disease pathogenesis. The diversity of endothelial cells (ECs) is transcriptionally evident and ECs undergo dynamic changes in gene expression during vessel growth and remodelling.Here, we investigated the role of the histone acetyltransferase HBO1 (KAT7), which is important for activating genes during development and histone H3 lysine 14 acetylation (H3K14ac). Loss of HBO1 and H3K14ac impaired developmental sprouting angiogenesis and reduced pathological EC overgrowth in the retinal endothelium. Single-cell RNA-sequencing of retinal ECs revealed an increased abundance of tip cells in Hbo1 deleted retinas, which lead to EC overcrowding in the retinal sprouting front and prevented efficient tip cell migration. We found that H3K14ac was highly abundant in the endothelial genome in both intra- and intergenic regions suggesting that the role of HBO1 is as a genome organiser that promotes efficient tip cell behaviour necessary for sprouting angiogenesis.

overall_design: Single cell RNA-seq profiling of P6 retinal endothelial cells from Hbo1 EC-deleted (n = 4) and heterozygous control mice (n = 4)

first: Zoe

middle: L

last: Grant

middle: F

first: Anne

middle: K

last: Voss

first: Leigh

last: Coultas


title: Transcription Factors HBIs-Mediated ROS Homeostasis Regulates Nitrate Signal Transduction in Arabidopsis

city: Qingdao

first: Xiaoqian

last: Chu

address: No. 72 Binhai Road

department: School of Life Sciences

institute: Shandong University

summary: Nitrate is both an important nutrient and a critical signaling molecule that regulates plant metabolism, growth, and development. Although several components of the nitrate signaling pathway have been identified, the molecular mechanism of nitrate signaling remains unclear. Here, we showed that the growth-related transcription factors HBI1 and its three closest homologs (HBIs) positively regulate nitrate signaling in plants. HBI1 is rapidly induced by nitrate through NLP6 and NLP7, which are master regulators of nitrate signaling pathway. Mutations in HBIs result in the reduced effects of nitrate on plant growth and approximately 22% nitrate-responsive genes no longer to be regulated by nitrate. HBIs increase the expression levels of a set of antioxidant genes to reduce the accumulation of reactive oxygen species (ROS) in plants. Nitrate treatment induces the nuclear localization of NLP7, whereas such promoting effects of nitrate are significantly impaired in the hbi-q and cat2cat3 mutants, which accumulate high levels of H2O2. These results demonstrate that HBI-mediated ROS homeostasis regulates nitrate signal transduction through modulating the nucleocytoplasmic shuttling of NLP7. Overall, our findings reveal that nitrate treatment reduces the accumulation of H2O2, and H2O2 inhibits nitrate signaling, thereby forming a feedback regulatory loop to regulate plant growth and development.

overall_design: Wild-type Col-0 seedlings, nlp7-1 and hbi-q mutants growing on medium with 7 mM KNO3 for 7 days were transferred to nitrogen-free medium for 2 days then treated with 10 mM KNO3 for 3 hours. To analyse the effects of H2O2 on nitrate regulated gene expression, Col-0 seedlings growing on medium with 7 mM KNO3 for 7 days were transferred to nitrogen-free medium for 2 days then treated with 10 mM KNO3 with or without 0.5 mM H2O2 for 3 hours or treated with H2O2 for 3 hours. Total RNA was extracted with Trizaol RNA extraction kit (Transgene), and mRNA sequencing libraries construction and sequencing on the BGISEQ-500 platform were performed at Beijing Genomics Institute. The sequence reads were mapped to the Arabidopsis genome using HISAT and Bowtie2 software. The gene reads count were calculated by htseq-count with default parameters, and differential gene expression was analysed using DESeq2 tool with generalized linear model. Differentially expressed genes were defined by 2-fold expression difference with false discovery rate (FDR) <0.05.

first: Jia-Gang

first: Ming-Yi

last: Bai

first: Xiang

last: Yu


title: Global chromatin relabeling accompanies spatial inversion of chromatin in rod photoreceptors

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

country: USA

institute: University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We used CUT&RUN sequencing technology for high-throughput profiling of histone modifications in murine rod photoreceptor cells during post-natal maturation. We generated genome-wide chromatin-state maps of mouse embryonic stem cells, and rod cells isolated from post-natal days 1, 7, 14, 21, and adult mice. We find that Histone H3 Lysine 9 methylation status changes over the course of rod cell maturation, accompanying the transition of nuclear architecture from "conventional" to "inverted" such that H3K9me2-labeled nuclear peripheral heterochromatin is relabeled with H3K9me3 and repositioned to the nuclear center, while transcriptionally active euchromatin is labeled with H3K9me2 and positioned at the nuclear periphery. Global chromatin relabeling is correlated with spatial rearrangement, suggesting a critical role for histone modifications, specifically H3K9 methylation, in nuclear architecture.

overall_design: Examination of histone modifications associated with heterochromatin and euchromatin in mouse embryonic stem cells and rod cells during rod photoreceptor maturation.

first: Cheryl

last: Smith

first: Andrey

last: Poleshko

first: Rajan

last: Jain

first: Jonathan

middle: A

last: Epstein


title: RNA-seq analysis of vehicle and DOPPA-treated human cord blood CD34+ cells

city: Indianapolis

first: Bin

last: Guo

state: Indiana

address: 950 W. Walnut Street

department: Microbiology & Immunology

institute: Indiana University

summary: In this study, we did RNA-sequencing analysis to check the transcriptome of vehicle and DOPPA-treated CD34+ cells after 4 days ex-vivo culture. We noticed that expression of many genes which encode cell surface proteins including ITGA6 (CD49f) were significantly up-regulated, FDR-adjusted p-value < 0.01 and the fold change (FC) > 2, by DOPPA treatment. Gene ontology (GO) analysis revealed that many GO functions related to cell surface or plasma membrane related GOs which all include ITGA6 were significantly enriched in up-regulated differentially expressed genes (DEGs) including ITGA6 after DOPPA treatment. These data suggest that DOPPA treatment promotes transcription of ITGA6.

overall_design: Identification of the differentially expressed mRNA profiles in vehicle and DOPPA expanded human cord blood CD34+ cells.

first: Hal

middle: E

last: Broxmeyer

first: Jun

last: Wan

first: Sheng

last: Liu


title: Nuclear speckle specific hnRNP DL loss lead to aging associated-cognitive decline by modulating MAPT alternative splicing

city: Hefei

first: Qingyang

last: Zhang

state: Anhui

address: No.443, HuangShan Road Shushan District

department: Division of Life Sciences and Medicine

institute: University of Science and Technology of China for School of Life Sciences

summary: We report the high-throughput sequencing for differential alternative splicing analyzation in hnRNP DL knockdown and control mice

overall_design: Examination of RNA alternative splicing patterns in hnRNP DL knockdown and control mice

first: Qiang

first: Juan


title: RNA-Sequencing of Ncs1+/+ and Ncs1-/- mouse brain tissues

city: New Haven

first: Barbara

last: Ehrlich

state: CT

address: 333 Cedar Street

department: Department of Pharmacology

institute: Yale University

summary: Analysis of genes and biological processes influenced by Neuronal calcium sensor 1 (NCS1) based on whole transcriptome analyiss of Ncs1+/+ (wildtype) and Ncs1-/- (knockout) mouse brain tissues, i.d. the frontal cortex and the hippocampus.

overall_design: 20 samples: 10 per genotype (Ncs1-/- vs. Ncs1+/+): 5 per brain region (frontal cortex vs. hippocampus)

first: Tom

middle: T

last: Fischer

first: Lien

middle: D

last: Nguyen


title: PRR11 unveiled as a top candidate biomarker within the RBM3-regulated transcriptome in pancreatic cancer

city: Dublin

first: Bruce

last: Moran

address: Nutley Lane, Dublin 4

department: Dept. of Pathology

country: Ireland

institute: St. Vincent's University Hospital

summary: The aim of this study was to unravel and functionally investigate RBM3-associated genes and proteins in pancreatic cancer cells in vitro, and to examine their expression and prognostic significance in human tumours.

overall_design: Next-generation sequencing was applied to compare transcriptomes of MiaPaCa2 and PANC-1 cells with and without RMB3 knockdown. The prognostic value of differentially expressed genes was examined in The Cancer Genome Atlas (TCGA). Top deregulated genes were then selected for further studies in vitro and for immunohistochemical analysis of corresponding protein expression in tumours from a clinically well-annotated consecutive cohort of patients with resected pancreatic and other periampullary cancers.

first: Sofie

middle: O

last: Hau

first: Karin

last: Jirström

first: Sophie

last: Cervin

first: Vilgot

last: Falk

first: Sara

last: Wahlin

first: Björn

last: Nodin

first: Jacob

last: Elebro

first: William

middle: M

last: Gallagher

first: Jakob

last: Eberhard

first: Emelie

last: Karnevi


title: Single cell sequencing analysis of adipose tissue stroma from lean and obese female mice

city: Oklahoma City

first: Elizabeth

last: Wellberg

state: Oklahoma

address: 975 NE 10th St, BRC 309

department: Pathology

institute: University of Oklahoma HSC

summary: We report the single cell sequencing data from subcutaneous adipose tissue CD29+ stromal cells (mesenchymal stem cells). Subcutaneous adipose tissue was collected from a mouse model of obesity and breast cancer anti-estrogen therapy. Lean and obese mice were ovariectomized, supplemented with estradiol, then maintained on estradiol, given tamoxifen, or estradiol was withdrawn for 7 weeks.

overall_design: Two to 3 mice per group (Low Fat or High Fat; E2, E2+Tamoxifen, E2 withdrawal) were used for tissue collection. Adipose was digested, stromal fraction was depleted of CD45+ and CD31+ cells, while CD29+ cells were retrieved by FACS. Approximately 10,000 cells per group of pooled samples (2-3 females pooled per diet and treatment group) were sequenced.

first: Austin

last: Gillen


title: miRNA and mRNA expression in placental tissue from high altitude pregnant women

city: xining

first: Tanna

last: Wuren

address: Kunlun Road No.16

institute: Qinghai University

type:
Expression profiling by array
Non-coding RNA profiling by array

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

platform_organism:
Homo sapiens
synthetic construct

overall_design: Refer to individual Series


title: Pluripotent stem cell-derived corneal endothelial cells as an alternative to donor corneal endothelium in keratoplasty

city: Baltimore

first: S. Amer

last: Riazuddin

address: 600 N. Wolfe street

institute: Johns Hopkins University

summary: Here, we evaluate the efficacy of cryopreserved human embryonic stem cell (hESC)-derived corneal endothelial cells (CECs) to form a functional monolayer of corneal endothelium (CE) in mammals (rabbits) and non-human primates (monkeys). We injected cryopreserved hESC-derived CECs in rabbits and monkeys either immediately after removing 8 mm of the central portion of the CE or a few days later when corneal edema developed. All clinical models developed deturgesced and clear corneas 2-3 weeks following the CEC injection and remained comparable to the CE of the untreated eye. Confocal scanning microscopy confirmed an intact structure of hexagonal/polygonal cells and immunohistochemical analysis illustrated a monolayer expressing barrier and pump function proteins in the regenerated CE. The necropsy examination confirmed no remarkable change in multiple tissues examined for teratoma formation. In conclusion, our data demonstrate the efficacy of cryopreserved hESC-derived CECs to form a functional CE on the denuded Descemet’s membrane.

overall_design: Next-generation RNA sequecning (RNA-Seq) of hESC-derived CECs at day 20 (non-cryopreserved) and cryopreserved hESC-derived CECs (cryopreserved for 40 days in liquid nitrogen) was performed. Briefly, three biological replicates for each of non-cryopreserved hESC-derived CECs and cryopreserved hESC-derived CECs were used for RNA-Seq library preparation. Total RNA was subjected to RNA-Seq library preparation using NEBNext Ultra II RNA Library Prep Kit for Illumina. The RNA-Seq bar-coded pooled libraries were sequenced (2 × 100 bp) using a HiSeq 2500 (rapid run mode) genome analyzer. The paired-end reads were assembled with SeqMan NGen (Ver. 12), using default parameters and aligned to the human reference genome (GRCh38.p11). The ArrayStar (Ver., 12; DNASTAR) was used for normalization, differential gene expression, and statistical analysis of mapped paired-end reads using the default parameters. FPKM was used for the normalization and quantification of gene expression.

first: S


title: miRNA expression in Placental Tissue from high altitude European and Tibetan women

summary: We used in silico analyses to identify the distinct transcriptome signatures of two populations living at high altitudes and identified potential mechanisms that underlie high-altitude adaptation. Data generated in this study indicate that placentas from Tibetan women are genetically distinct from European women at high altitudes, and appear to be protected from hypoxia and stress.

overall_design: Examination of transcriptome level in placenal tissue from 2 different high altitude population

first: Tenzing

last: Noryung

first: Martha

last: van Patot

first: Liu

last: Huifang

first: Xu

last: Qiying

last: Juanli

first: Wang

last: Zhuoya

first: Yanjun

last: Wang

first: Wuren

last: Tana

first: Ge

last: Ri-Li


title: Gene expression in Placental Tissue from high altitude European and Tibetan women

overall_design: Examination of transcriptome level  in  placenal tissue from 2 different high altitude population


title: RNA-seq studies

city: Xi'an

first: Jiejie

last: Geng

state: Shanxi

address: Changle West road

department: Cell biology department

institute: The Fourth Military Medical University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: RNA-seq Analysis of control and CyPA-stimulated BEAs-2B cells Transcriptomes

summary:
Purpose: The goals of this study are to compare the difference between control and CyPA-stimulated BEAs-2B cells Transcriptomes
Methods: After receiving anesthesia with pentobarbital sodium, each mouse of the WT group, hCD147 group, and hACE2 group was infected with SARS-CoV-2 by nasal drip at a dose of 3 × 105 TCID50. The lung tissues were take for RNA-seq at 2 dpi.
Results: CyPA-stimulated BEAs-2B cells showed upregulated expression of a variety of proinflammatory cytokines and chemokines, including IL6, IL1b, MCP-1, CXCL1 and CXCL2, as well as several AP-1 family members, including c-FOS, FOSL1 and FOSL2 that promote the transcription of multiple cytokine genes during inflammation
Conclusions: CyPA induces cytokine expression through the CD147-mediated MAPK pathway

overall_design: mRNA profiles of  control and CyPA-stimulated BEAs-2B cells Transcriptomes

first: Zhi-Nan

last: Chen

first: Ping

last: Zhu

first: Huijie

last: Bian

first: Liang


title: RNA-seq Analysis of wild type, hACE2 and hCD147 mice lung tissues Transcriptomes after infection with SARS-CoV-2

summary:
Purpose:
The goals of this study are to compare the difference between WT and hCD147 mice, hACE2 and hCD147 mice lung tissues Transcriptomes after infection with SARS-CoV-2

Methods:
After receiving anesthesia with pentobarbital sodium,
each mouse of the WT group, hCD147 group, and hACE2 group was infected with SARS-CoV-2 by nasal drip at a dose of 3 x 10^5 TCID50. The lung tissues were take for RNA-seq at 2 dpi.
each mouse of the hCD147 group, and hACE2 group was infected with SARS-CoV-2 by nasal drip at a dose of 3 x 10^5 TCID50. The lung tissues were take for RNA-seq at 2 dpi.

Results:
RNA-seq of lung homogenates from C57BL/6 and hCD147 mice at 2 d.p.i. showed 354 upregulated and 175 downregulated genes). hCD147 mice mediated strong inflammatory responses, including Th17 cell responses, the NF-kappaB pathway and MAPK pathway, etc. The levels of cytokines and chemokines were increased in the lung of hCD147 mice, such as IL6, IL10, ILbeta, CXCL1, CXCL2, CCL2, etc.
Analysis of RNA-Seq data of hACE2 mice versus hCD147 mice showed that hACE2 mice had stronger antiviral responses, including type I IFN and IFNalpha/IFNbeta responses, while hCD147 mice showed activation of multiple proinflammatory pathways, which is consistent with clinical features of COVID-19 patients. The significantly upregulated genes during SARS-CoV-2 infection of hACE2 mice enriched in cellular response to IFN-?. The upregulated genes in SARS-CoV-2-infected hCD147 mice were enriched secretory proteins, including ILbeta, IL6 and CXCL1.

Conclusions:
CD147 mediates potent inflammatory responses in SARS-CoV-2 infection.
RNA-seq of lung homogenates from hACE2 and hCD147 mice at 2 d.p.i. showed 354 upregulated and 175 downregulated genes). hCD147 mice mediated strong inflammatory responses, including Th17 cell responses, the NF-kappaB pathway and MAPK pathway, etc. The levels of cytokines and chemokines were increased in the lung of hCD147 mice, such as IL6, IL10, ILbeta, CXCL1, CXCL2, CCL2, etc.

overall_design:
Lung mRNA profiles of  Wild Type and hCD147 mice lung tissues after infection with SARS-CoV-2
Lung mRNA profiles of  hACE2 and hCD147 mice lung tissues after infection with SARS-CoV-2


title: Analysis of differential expression genes in the lung of Eif4b CKO mice and wild type mice

city: Beijing

first: Biao

address: NO. 1 Beichen West Road, Chaoyang District

institute: Institute of Microbiology, Chinese Academy of Science

summary: To identify important differential expression genes（mRNA） in the lung of  Eif4b CKO mice and wild type mice with or without IAV infection, transcriptome RNA sequencing in the lungs of uninfected or infected eIF4B CKO mice and control mice was performed

overall_design: Lungs of control mice or eIF4B CKO mice used for transcriptome RNA-sequencing were from three independent groups of WSN-infected mice (5×104 PFU, 48 hpi) or uninfected mice

first: Ji-Long


title: RNAseq of isolated astrocytes and microglia from APPPS1E4fl/fl mice following astroycte APOE removal

city: St. Louis

first: Jason

last: Ulrich

address: 425 S. Euclid

institute: Washington University

summary: The e4 allele of the apolipoprotein E (APOE) gene is the strongest genetic risk factor for late-onset Alzheimer's disease and has been shown to increase amyloid pathology relative to the presence of the e2 and e3 alleles. In the brain, apoE is primarily produced by astrocytes and under pathological conditions also by microglia. The cell-type-specific role of apoE in amyloid pathology, especially after amyloid plaque deposition, has not been fully elucidated. We generated APPPS1-21/Aldh1l1-Cre/ERT2/apoE4flox/flox and APPPS1-21/apoE4flox/flox mice. At 3.8-months-of-age, during the phase of rapid plaque growth, we administered tamoxifen to reduce astrocytic APOE4 and assessed mice at 6-months-of-age. One day before tamoxifen treatment, mice were injected with methoxy-X04, a blood-brain-barrier permeant fluorescent marker that labeled the pre-existing fibrillar amyloid plaques. By using this strategy, we were able to characterize pre-existing plaques prior to the loss of astrocytic APOE4 and to also analyze newly-formed amyloid plaques after the loss of astrocytic APOE4. Interestingly, astrocytic APOE4 deletion strongly reduced pre-existing plaques. It also prevented new plaque formation and decreased glial reactivity. Importantly, the removal of astrocytic APOE4 resulted in enhanced microglial and astrocytic phagocytic ability, which may contribute to the reduction of the amyloid pathology.

overall_design: Microglia or astrocytes were sorted from APPPS1::APOE4fl/fl::ALDH1L1-CreERT (n=4), APPPS1::APOE4fl/fl (n=4), APOE4fl/fl (n=2), and APOE4::ALDH1L1-CreERT (n=2)  All mice were treated with tamoxifen at 3.8 months of age and cells isolated by FACS 10 days later using using anti-Cd11b-Cy7 antibodies for microglia and anti-ACSA-2-PE antibodies for astrocytes.

first: David

last: Holtzman

first: Chao


title: Hi-C profiling of cancer spheroids identifies 3D-growth-specific chromatin interactions in breast cancer endocrine resistance

city: Milwaukee

first: Victor

last: Jin

state: WI

address: 8701 Watertown Plank Rd

department: IHE

institute: Medical college of Wisconsin


title: Modeling sporadic Alzheimer’s disease in human brain organoids under serum exposure

city: Duarte

first: wei

last: chen

state: CA

address: 1500 E Duarte Rd

department: Cancer Biology-BRI

institute: City of Hope National Medical Center

summary: Although sporadic AD (sAD) accounts for the majority of AD cases, the underlying mechanisms remain largely unknown. Here we modeled sAD using human induced pluripotent stem cell (iPSC)-derived three-dimensional brain organoids. We exposed brain organoids to serum to mimic the serum exposure consequence of BBB breakdown in AD patient brains. The serum-exposed brain organoids were able to recapitulate AD-like pathologies, including increased Aβ aggregates and p-Tau level, synaptic loss, and impaired calcium signaling and neural network. Serum exposure increased Aβ and p-Tau levels through inducing BACE and GSK3α/β levels, respectively. In addition, single-cell transcriptomic analysis of brain organoids revealed that serum exposure reduced synaptic function in both neurons and astrocytes, and induced immune response in astrocytes. The human brain organoid-based sAD model established in this study could provide a powerful platform for both mechanistic study and therapeutic development.

overall_design: 14048 brain organoids (BO2) and ADRC28 brain organoids (BO3) were treated without (control) or with 10% human serum (8748 or 3821) for 13-14 days and then were harvested at day 94-95 for scRNA-seq

first: Xianwei

first: Yanhong

last: Shi


title: RNA-seq analysis of freshly isolated and ex-vivo cultured human cord blood CD34+ cells

first: Bin

last: Guo

summary: RNA-seq analysis was performed to compare differentially expressed genes in freshly isolated and ex-vivo cultured human cord blood CD34+ cells. Mitochondrion related genes are upregulated in CD34+ hematopoietic stem and progenitor cells upon ex vivo culture. In vivo transplantation experiments demonstrate that stemness of CD34+ cells is significantly decreased due to oxidative stress induced by ex vivo culture.

overall_design: Freshly isolated cord blood CD34+ cells (Group 0) and day-4 ex-vivo cultured cord blood CD34+ cells (Group 4) are subjected to RNA-seq analysis.

first: Hal

last: Broxmeyer

first: Jun

last: Wan

first: Sheng

last: Liu


title: The Polycomb protein RING1B enables estrogen-mediated gene expression by promoting enhancer-promoter interaction and R-loop formation

city: Miami

first: Lluis

last: Morey

state: FL

department: Sylvester Comprehensive Cancer Center

institute: University of Miami Miller School of Medicine

summary: Polycomb complexes have traditionally been prescribed roles as transcriptional repressors, though increasing evidence demonstrate they can also activate gene expression. However, the mechanisms underlying positive gene regulation mediated by Polycomb proteins are poorly understood. Here, we show that RING1B, a core component of Polycomb Repressive Complex 1, regulates enhancer-promoter interaction of the bona fide estrogen-activated GREB1 gene. Systematic characterization of RNA:DNA hybrid formation (R-loops), nascent transcription, and RNA Pol II activity upon estrogen administration revealed a key role of RING1B in gene activation by regulating R-loop formation and RNA Pol II elongation. We also found that the estrogen receptor (ER) and RNA are both necessary for full RING1B recruitment to estrogen-activated genes. Notably, RING1B recruitment was mostly unaffected upon RNA Pol II depletion by triptolide. Our findings delineate the functional interplay between RING1B, RNA, and ER to safeguard chromatin architecture perturbations required for estrogen-mediated gene regulation, and highlight the crosstalk between steroid hormones and Polycomb proteins to regulate oncogenic programs.

overall_design: ChIP-seq of RING1B, ERa, and RNA Pol II in T47D cells treated with DMSO or Triptolide (10 uM) for 9 hours in HD and after 45' of E2 treatment. RING1B and ERa ChIP-seq are provided in duplicates. Pair-end ATAC-seq of T47D shCtrl and shRING1B cells in HD and after45' of E2 in duplicates. RNA-seq of T47D shCtrl and shRING1B cells in HD and after 45' of E2 in duplicates. RING1B and ERa rChIP of T47D cells treated with DMSO for 9 hours followed by E2 for 45' provided in duplicates. DRIP-seq of T47D cells in HD and after 45' of E2 along with negative controls. DRIP-seq of T47D shCtrl and shRING1B cells in HD and after 45' of E2 along with negative controls. 4C-seq of T47D shCtrl and shRING1B cells in HD and after 45' of E2.

first: Yusheng

last: Zhang

first: Tong

first: Fenghua

last: Yuan

first: Liliana

last: Garcia-Martinez

first: Kytae

last: Lee

first: Stephanie

last: Stransky

first: Simone

last: Sidoli

first: Ramiro

last: Verdun

first: Yanbin

first: Zheng


title: Neurotensin regulates proliferation and stem cell function in the small intestine in a nutrient-dependent manner

city: Lexington

first: Mark

last: Evers

state: Kentucky

address: 800 Rose Street

department: College of Medicine

institute: University of Kentucky

summary:
Background & Aims: Intestinal stem cells (ISCs) are sensitive to dietary alterations and nutrient availability. Neurotensin (NT), a gut peptide localized predominantly to the small bowel and released by fat ingestion, stimulates the growth of intestinal mucosa under basal conditions and during periods of nutrient deprivation, suggesting a possible role for NT on ISC function.
Methods: Lgr5-EGFP, NT wild type (Nt+/+) and Lgr5-EGFP, NT knockout (Nt-/-) mice were fed ad libitum (AL) or fasted for 48 h. Small intestine crypts were examined by RNAseq analysis.
Results: Loss of NT impaired crypt cell proliferation and ISC function in a manner dependent on nutrient status. Under nutrient-rich conditions, NT stimulated the expression of genes that promote cell cycle progression, leading to crypt cell proliferation. Under conditions of nutrient depletion, NT stimulated WNT/β-catenin signaling and promoted an ISC gene signature, leading to enhanced ISC function. NT was required for the induction of WNT/β-catenin signaling and ISC-specific gene expression during nutrient depletion, and loss of NT reduced crypt cell proliferation and impaired ISC function and Lgr5 expression in the intestine during fasting.
Conclusion: Collectively, our findings establish an evolutionarily conserved role for NT in ISC maintenance during nutritional stress.

overall_design: Male and female NT+/+ and NT-/- mice were fed ad libitum or fasted for 48h and then intestinal crypts collected for RNA isolation and RNA sequencing. NT+/+ ad libitum fed mice served as controls.

last: Rock

first: Yuanyuan

last: Wu

first: Chi

last: Wang

first: B


title: ChIP seq for GATA-1 and HDAC1 in G1E cells with wild type GATA-1 or mutant

city: Hershey

first: Bowen

last: Yan

address: HERSHEY MED CTR 500 UNIVERSITY DRIVE 500 UNIVERSITY DRIVE

institute: PENNSYLVANIA STATE UNIV

summary: The transcription factor GATA-1 is essential for erythroid and megakaryocytic cell differentiation and maturation. Previous reports show that GATA-1 is modulated through acetylation modification and through FOG-1 mediated indirect intereaction with HDAC1/2 containing NuRD corepressor complexes. In this study, we found that NuRD does not deacetylate GATA-1. However, HDAC1 alone can efficiently deacetylates GATA-1 and the direct interaction of HDAC1 and GATA-1 is required for the deacetylation. Two arginines within GATA-1 linker region are important for this interaction and arginine to alanine mutations (2RA mutant) largely reduces GATA-1 binding to HDAC1 in FOG-1 independent manner. GATA-1 2RA mutant were then introduced into G1E cells, a GATA-1-null erythroid progenitor cells. The 2RA mutant is acetylated but fails to induce erythroid differentiation. Gene expression analysis shows that GATA-1 2RA mutant affects GATA-1 function in both GATA-1 activated and repressed genes. The gene expression pattern partially overlap with gene expression profile of GATA-1V205M, a GATA-1 mutant with defective FOG-1 binding. ChIP-seq analysis further reveal that 2RA mutation largely reduced GATA-1 chromatin binding, most profoundly at gene promoter regions. HDAC1 recruitment on those promoters are also strongly reduced. These results revealed that GATA-1 recruits HDAC1 to GATA-1 regulated gene promoters and HDAC1 is required for GATA-1 mediated transcription regulation.

first: Yi

last: Qiu


title: Single cell RNA-seq for GATA-1 wildtype and 2RA mutation Knockin mice bone marrow

summary:
Purpose: To compare bone marrow cell population and gene regulation changes in GATA-1 mutation Knockin mice compared with wild type mice
Methods: Flow cytometry sorting mouse bone marrow cells (Lin- Kit+) from GATA-1 mutation Knockin mice and wild type mice were collected and performed single cell RNAseq analysis
Results: cell population and gene regulation changes in GATA-1 mutation Knockin mice and wild type mice bone marrow cells were compared


title: Hi-C profiling of cancer spheroids identifies 3D-growth-specific chromatin interactions in breast cancer endocrine resistance [RNA-Seq]

first: Victor

last: Jin

summary: Organoids or spheroids have emerged as a physiologically relevant in vitro preclinical model to study patient-specific diseases. A recent study used spheroids of MCF10 cells to model breast cancer progression and identified targetable alterations more similar to those in vivo. Thus, it is practical and essential to explore and characterize the spheroids of the commonly used human breast cancer (BC) cells. This study conducted Hi-C analyses in three-dimensional (3D) spheroids of MCF10A, MCF7 and MCF7TR cells and compared TADs and looping genes with those in 2D monolayers. We found that chromatin domains and looping genes’ strength have drastically changed during the 3D culture growth, although we identified very similar numbers of TADs and looping genes. We further identified novel 3D growth-specific looping genes within Hippo relevant pathways, of which two genes showed potential prognostic values in measuring the outcome of the endocrine treatment. We finally confirmed a few selected Hippo relevant pathways genes with enhanced looping in breast cancer patient tissues’ organoid. Hence, our work has provided significant insights into our understanding of 3D-growth-specific chromatin architecture in tamoxifen-resistant breast cancer.

overall_design: RNA-seq experiment of 3 cell types in 2D monolayers or 3D spheroids, 3 biological replicates for each condition.

first: Jingwei

last: Li

first: Lavanya

last: Choppavarapu


title: Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [RNA-seq]

city: Shanghai

first: Linna

last: Peng

address: Dong'an Road

institute: Fudan University

summary: Transcription machinery progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Yet its mechanistic understanding in human cells remains incomplete. Here we utilize rapid degradation system and reveal crucial function of SPT5 in maintaining cellular and chromatin Pol II levels. Rapid SPT5 depletion causes a pronounced reduction of paused Pol II at promoters and enhancers, distinct from NELF degradation resulting in short-distance paused Pol II redistribution. Most of genes exhibit down- but not upregulation, accompanied by greatly impaired transcription activation and altered chromatin landscape at enhancers, and severe Pol II processivity defects at gene bodies. Phosphorylation of KOWx-4/5- linker potentiates pause release and is antagonized by Integrator-PP2A (INTAC) targeting SPT5 and Pol II. Our findings position SPT5 as an essential positive regulator of global transcription by controlling cellular Pol II levels, enhancer activation and landscape, paused Pol II stability, elongation processivity and termination in human.

overall_design: We performed PRO-seq, ATAC-seq, RNA-seq, ChIP-seq, or TT-seq to investigate the role of SPT5 in regulating transcription. In this study, samples for each condition were collected in biological duplicates. Cells were treated with dTAG13 for 3, 12,or 24 hours, the corresponding control cells were treated for the same duration with vehicle only (DMSO) at the same vol/vol dilution.

first: Shibin

last: Hu

first: Zhenning

first: Aixia

last: Song

first: Fei

last: Chen


title: RNAseq of Wild Type and GATA-1 mutants in G1E cells

summary:
Purpose: To compare gene regulation changes in GATA-1 mutant compared with wild type
Methods: G1E cells with wild type GATA-1 or mutant were induced by β-estrodiol
Results: We mapped the sequence reads to the mouse genome (build mm10) with TopHat workflow. Some of altered expression of genes was confirmed with qRT–PCR.

overall_design: Gene expression profile of G1E cells with Wild Type or GATA-1 mutants.


title: Dual RNAseq of murine alveolar macrophage cell line MH-S confronted with resting spores of Lichtheimia corymbifera JMRC:SF:09682

city: Jena

first: Patricia

last: Sieber

address: Adolf-Reichwein-Straße 23

country: Germany

institute: HKI

summary: During the infection process, both the host and the pathogen undergo a dynamic cascade of events that result in altered gene expression patterns (Westermann et al. 2012). With dual-RNA analysis, the complex interaction between a pathogen and its host during infection can be revealed simultaneously at their RNA levels (Westermann et al. 2012). Therefore, dual-transcriptomic analysis on JMRC:FSU:09682 and MH-S was performed to understand the pathogenesis at the genetic level to identify what kind of stresses that L. corymbifera encounter as well as the transcriptional response of macrophages during the infection. L. corymbifera (JRMC:FSU:09682) was cultivated for 7 days in KK1 medium (Kraibooj et al. 2014) at 37 °C . Murine alveolar MH-S macrophages (ATCC: CRL-2019) were cultivated in RPMI-1640 supplemented with 10% heat inactivated fetal bovine serum at 37 °C in 5 % CO2. Macrophages were seeded in 6 well plates at 106 cells per well to adhere overnight. Macrophages were infected with spores at a MOI (Multiplicity of Infection) of 5. After 3 hr of co-incubation with MH-S, extracellular spores were removed by at least 3 washing steps with pre-warmed RPMI-1640 (PAA Laboratories) and incubated for 13 hr in prior to the RNA extraction procedure. Controls in these experiments were fungus grown for 16 hours without macrophages and macrophages without fungal spores. Fungal RNA was isolated using RiboPure Yeast Kit (Thermo Fisher) and macrophage RNA was isolated with the RNeasy Mini kit (Qiagen), according to the manufacturers’ instructions. The concentration and purity of RNA samples were assessed using a NanoDrop spectrophotometer and Agilent 2100 bioanalyzer. A total of 681 L. corymbifera genes were differentially expressed during the co-infection with macrophages, with 629 down- (data not shown) and 52 up-regulated (Table 4.1). In order to systematically analyse the function of the differentially expressed genes (DEG), GO enrichment analyses were performed using FungiFun2.

sample_organism:
Mus musculus
Lichtheimia corymbifera

platform_organism:
Mus musculus
Lichtheimia corymbifera

overall_design: 6 samples in total: Time point 0 with 3 replicates of Lcor strain JMRC:SF:09682; Time point 16 h with 3 replicates of Lcor strain JMRC:SF:09682 in coculture with murine alveolar macrophage cell line MH-S

first: Kerstin

last: Voigt

first: Volker

middle: U

last: Schwartze

first: Hea-Reung

last: Park

first: Hans-Martin

last: Dahse

first: Philipp

last: Kaemmer

first: Sascha

last: Brunke

first: Bernhard

last: Hube

first: Jörg

last: Linde


title: AKT signaling promotes epigenetic reprogramming via upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation

city: Sagamihara

first: Yoichi

last: Sekita

state: Kanagawa

address: 1-15-1 Kitasato, Minami-ku

department: Biosciences

country: Japan

institute: Kitasato University School of Science

summary: Phosphoinositide-3 kinase (PI3K)/AKT signaling participates in cellular proliferation, survival, and tumorigenesis as well as cellular reprogramming including generation of induced pluripotent stem cells (iPSCs). In this study, we revealed that activation of AKT in somatic cells undergoing reprogramming enhances epigenetic reprogramming. Activated AKT in reprogramming cells triggers elevated anabolic glucose metabolism, and, accordingly, increases the level of α-ketoglutarate (αKG) which is an essential cofactor for the enzymatic activity of the 5-methylcytosine (5mC) dioxygenase TET. Additionally, the level of TET was upregulated. Consistent with upregulated KG production and TET, we observed a genome-wide increase in 5-hydorxymethylcytosine (5hmC) which is an intermediate in the DNA demethylation process. Moreover, DNA methylation level at ES-cell super-enhancers of pluripotency-related genes was significantly decreased, leading upregulation of associated genes. Taken together, our results indicate that AKT signaling is associated with epigenetic regulation by hyperactivating TET at catalytical and transcriptional levels during the somatic cell reprogramming.

overall_design: mRNA profiles of reprogramming mouse embryonic fibroblasts (MEFs) with or without AKT activation. Cells were sampled 8 days after transduction of reprogramming factors (Oct4, Sox2, Klf4) and AKT-MER (AKT fused with modified estrogen receptor). AKT can be activated by administrating 4-hydroxytamoxifen (4OHT).

first: Yuki

last: Sugiura

first: Akari

last: Matsumoto

last: Kawasaki

first: Kazuya

last: Akasaka

first: Ryo

last: Konno

first: Momoka

last: Shimizu

first: Toshiaki

last: Ito

first: Eiji

last: Sugiyama

first: Terushi

last: Yamazaki

first: Eriko

last: Kanai

first: Toshinobu

last: Nakamura

first: Makoto

last: Suematsu

first: Fumitoshi

last: Ishino

first: Yoshio

last: Kodera

first: Takashi

last: Kohda

first: Tohru

last: Kimura


title: AKT signaling promotes epigenetic reprogramming via upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation.

last: Sekita

summary: Phosphoinositide-3 kinase (PI3K)/AKT signaling participates in cellular proliferation, survival, and tumorigenesis as well as cellular reprogramming including generation of induced pluripotent stem cells (iPSCs). In this study, we revealed that activation of AKT in somatic cells undergoing reprogramming enhances epigenetic reprogramming. Activated AKT in reprogramming cells triggers elevated anabolic glucose metabolism, and, accordingly, increases the level of α-ketoglutarate (αKG) which is an essential cofactor for the enzymatic activity of the 5-methylcytosine (5mC) dioxygenase TET. Additionally, the level of TET was upregulated. Consistent with upregulated KG production and TET, we observed a genome-wide increase in 5-hydorxymethylcytosine (5hmC) which is an intermediate in the DNA demethylation process. Moreover, DNA methylation level at ES-cell super-enhancers of pluripotency-related genes was significantly decreased, leading upregulation of associated genes. Taken together, our results indicate that AKT signaling is associated with epigenetic regulation by hyperactivating TET at catalytical and transcriptional levels during the somatic cell reprogramming.

overall_design: mRNA profiles of reprogramming mouse embryonic fibroblasts (MEFs) with or without AKT activation. Cells were sampled 10 days after transduction of reprogramming factors (Oct4, Sox2, Klf4) and AKT-MER (AKT fused with modified estrogen receptor). AKT can be activated by administrating 4-hydroxytamoxifen (4OHT).


title: The effects of weight cycling on the metabolic homeostasis

city: Wuhan

first: Yu

last: Sun

address: Luojiashan Street

institute: Wuhan University

summary:
Purpose: To investigate the effects of weight cycling on the metabolic homeostasis
Methods: C57BL/6 mice were fed with high fat diet (HF) (60% kcal fat; Research Diets Inc., New Brunswick, NJ) or low fat diet (LF) (10% kcal fat; Research Diets Inc.) at 6-week-old. Nine weeks after in HF, a part of mice was switched to LF for one week followed by one week HF as one cycle, and the mice under this one week diet switch protocol for 10 cycles were named HF-LF cycled mice, while the left part of mice under continuously HF-feeding were named HF mice. The mice kept in the continuously LF-feeding were named LF mice
Results: We identified many changed genes in the eWAT by RNA-sequencing.
Conclusions: This finding provides a signaling in eWAT upon weight cycling

overall_design: 6 samples (F-L rep1, F-L rep2, F-H rep1, F-H rep2, F-H-L rep1, F-H-L rep2) for mRNA sequencing

first: Ling

last: Zheng

first: Kun

last: Huang


title: A novel transcription factor, OsERF106, negatively regulates salinity tolerance in rice by disrupting ion homeostasis

city: Taipei

first: MenChi

last: Chang

state: Taiwan (R.O.C.)

address: No. 1, Sec. 4, Roosevelt Rd.

department: Agronomy

country: Taiwan

institute: National Taiwan University

summary: Background: Transcription factors (TFs), such as ERFs (Ethylene Responsive Factors), are important for regulating plant growth, development, and plant responses to abiotic stress. Notably, over half of the rice ERF-X group members are stress-responsive genes, including OsERF106. However, their regulatory roles in abiotic stress responses remain poorly understood. Results: The OsERF106, a salinity-induced gene of unknown function, was differently annotated in the RAP-DB and MSU RGAP. In this study, we isolated a novel (i.e., previously unannotated) OsERF106 gene and investigated its role in regulating growth and the response to salinity stress in rice. This OsERF106 is expressed in germinating seeds, primary roots, and developing flowers. Overexpression of the novel OsERF106 can cause a retardation of growth, a relatively high level of both MDA and ROS contents, a depression of CAT activity, and an overaccumulation of both Na+ and K+ ions in the transgenic rice shoots. Meanwhile, the expression of OsHKT1.3 is down-regulated in the shoots of transgenic seedlings grown under both normal and NaCl-treated conditions, while the expression of OsAKT1 is up-regulated in the same tissues grown under NaCl-treated conditions. Further analysis by microarray and qPCR indicated that the expression of several abiotic stress-responsive genes, such as OsABI5 and OsSRO1c, is also changed in the shoots of transgenic rice grown under either normal or NaCl-treated conditions. Conclusion: The novel OsERF106 negatively regulates shoot growth and salinity tolerance in rice through the disruption of ion homeostasis and modulation of stress-responsive gene expression.

overall_design: Gene expression of 8-day-old TNG67 and overexpressed OsERF106 in rice was measured.  The experiment was conducted by three biological repeats.

first: Chen

last: Tsung-Yang

first: Chien

last: Tzu-Cheng

first: Chang

last: Men-Chi


title: Genome-wide identification of altered m6A-related transcript profiles for vascular tissue in septic rats

first: Jinghua

last: Yang

address: 32 North Third Ring Road West, Haidian District, Beijing

institute: Beijing Zhiyun data technology co. LTD

summary: Sepsis is the leading cause of death in hospital intensive care units. Recent studies have shown that N6-methyladenosine (m6A) modification promotes the inflammatory response, and we evaluated the effect of lipopolysaccharide (LPS) on aortic m6A modifications in mRNAs and lncRNAs.

overall_design: LC-MS/MS was used to verify the m6A global level of LPS and Control groups. High-throughput microarray was performed on the aortic tissue to identify m6A differentially methylated lncRNAs and mRNAs. m6A single-base site qPCR analysis was used to verify the microarray data. Gene Ontology (GO) enrichment and Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis were used to investigate the biological functions. Establishment of competing endogenous RNA (ceRNA) and protein-protein interaction were performed to study the molecular interactions of these molecules. Quantitative real-time polymerase chain reaction (RT-qPCR) analysis was used to verify the m6A modification related genes.

first: Zhujun

last: Shen

first: Yechen

last: Han

first: Muwen

last: Nie

first: Yining

last: Wang

first: Ruolan

last: Xiang

first: Hongzhi

last: Xie


title: Controlling tissue patterning by translational regulation of signaling transcripts through the core translation factor eIF3c [I]

city: Stanford

first: Gun Woo

last: Byeon

address: 279 Campus Dr., Beckman Center B309

institute: Stanford University

summary: Although gene expression is tightly regulated during embryonic development, the impact of translational control has received less experimental attention. Here, we find that eukaryotic translation initiation factor-3 (eIF3) is required for Shh-mediated tissue patterning.  Analysis of loss-of-function  eIF3 subunit c (Eif3c) mice reveal a unique sensitivity to the Shh receptor Patched 1 (Ptch1) dosage. Genome-wide in vivo enhanced cross-linking immunoprecipitation sequence (eCLIP-seq) shows unexpected specificity for eIF3 binding to a pyrimidine rich motif present in subsets of 5’-UTRs and a corresponding change in the translation of these transcripts by ribosome profiling in Eif3c loss-of-function embryos. We further find that while Eif3c loss-of-function embryos do not show a global decrease in protein synthesis, translation of Ptch1 through this pyrimidine rich motif is specifically sensitive to eIF3 amount. Altogether, this work uncovers hidden specificity of housekeeping translation initiation machinery for the translation of key developmental signaling transcripts.

overall_design: Ribosome profiling (Ribo-seq)/RNA-seq

first: Kotaro

last: Fujii

first: Olena

last: Zhulyn

first: Gun

middle: W

first: Craig

last: Kerr

first: Naomi

last: Genuth

first: Erin

last: Walsh

first: Maria

last: Barna


title: The circular RNA hsa_circ_000780 as a potential molecular diagnostic target for gastric cancer

status: Public on Sep 28 2021

city: Haikou

first: JIAN

last: SONG

state: Hainan

address: 6 Changbin West 4th Street, Xiuying District

institute: the Affiliated cancer Hospital of Hainan Medical 6 University

summary: The present study aimed to identify a specific circular RNA (circRNA) for early diagnosis of gastric cancer (GC).

overall_design: Firstly, four cases of gastric cancer and their adjacent tissues were selected, and the differentially expressed circRNA was screened by circRNA microarray. Eight circRNAs with the greatest differentiation were selected, and their accuracy was further verified by RT-PCR. The sample size was expanded to screen the circRNA specific for gastric cancer

first: Jian

last: Song


title: Mnt Represses Epithelial Identity To Promote Epithelial to Mesenchymal Transition

city: Odense M

first: Vijay

last: Tiwari

state: Denmark

address: Campusvej 55

department: Institut for Molekylær Medicin (IMM)

country: Denmark

institute: Queen’s University Belfast

summary: The multi-step process of epithelial to mesenchymal transition (EMT), whereby static epithelial cells become migratory mesenchymal cells, is heavily involved in development, wound healing, and disease states. Despite the major involvement of basic helix-loop-helix (bHLH) transcription factors (TFs) in cell-fate determination, few have examined them for their involvement in fundamental processes that require EMT. Here, we have identified Max network transcription repressor (MNT) as a potent EMT promoting TF in mammary epithelium. We show that depletion of MNT blocked TGF?-induced phenotypic changes, and transcriptomic analysis revealed that MNT is a transcription repressor of epithelial identity. We show that MNT mediates repression of epithelial identity via direct interaction with HDAC1. Lastly, we show that MNT and its target genes are heavily expressed in EMT-High breast cancer, with MNT required for breast cancer cell migration. Taken together, these findings establish MNT as a critical regulator of cell-fate determination and the EMT transcriptome.

overall_design: Transcriptomic analysis of NMuMG cells following Mnt depletion during TGFbeta-induced EMT

first: Deborah

middle: P

last: Lavin

first: Leila

last: Abassi

first: Mohammed

last: Inayatullah


title: ACSA-2 and GLAST classify subpopulations of neurogenic and glial restricted cerebellar precursors

city: Bergisch-Gladbach

first: Stefan

last: Tomiuk

address: Friedrich-Ebert-Str. 68

department: Bioinformatics

institute: Miltenyi Biotec GmbH

summary: Neurogenic astroglia-like cells of the prospective white matter (PWM) generate interneurons and astroglia during cerebellar development. However, the characterization of PWM subpopulations is still insufficient. Here we show that ACSA-2 (Astrocyte Cell Surface Antigen-2) is an intrinsic marker of astrocyte-committed precursors. In the developing cerebellum, the ontogeny of ACSA-2+ astrocytes revealed this epitope to be exclusively expressed by PWM cells. By contrast, in the adult brain, ACSA-2 is observed on parenchymal astrocytes, fibrous astrocytes of the white matter and at low level on Bergmann glia. In combination with GLAST, a marker for astroglia-like progenitors, we addressed the characteristics of neurogenic (ACSA-2-/GLAST+) and astrocyte-committed (ACSA-2+/GLAST+) precursors using transcriptomics and cell transplantation assays. Gene expression analyses identified major differences in genes related to the maturation status of astrocytes, their potential to generate interneurons and genes required for Bergmann glia specification. Transplantation assays further confirmed a divergent differentiation potential: ACSA-2+/GLAST+ cells, on the one side, differentiate into astrocytes and oligodendrocytes but not into Bergmann glia or neurons when transplanted into the neonatal cerebellum. On the other side, ACSA-2-/GLAST+ progenitors were able to generate interneurons and all the glial phenotypes. Moreover, ACSA-2-/GLAST+ progenitors even maintained the neurogenic potential when transplanted into the adult cerebellum. In conclusion, this work reports about ACSA-2, a marker for glial-restricted precursors of the PWM that in combination with GLAST enables for the discrimination and isolation of neurogenic and astrocyte-committed progenitors of the neonatal cerebellum.

overall_design: The dataset comprises two different sample groups with three biological replicates each. All samples were obtained from neonatal (P1-P3) cerebellar tissue (wild-type mice). Samples were sorted for ACSA-2+/GLAST+ and ACSA-2-/ GLAST+ cells using magnetic cell isolation. Microarray analysis was performed on the Agilent Whole Mouse Genome Oligo Microarray 8x60K platform.

first: Christina

middle: G

last: Kantzer

first: Elena

last: Parmigiani

first: Michail

last: Knauel

first: Melanie

last: Jungblut

first: Annalisa

last: Buffo

first: Andreas

last: Bosio


title: The effect of pyruvate starvation under normal- and high-glucose conditions

city: Hachioji

first: Hideji

last: Yako

state: Tokyo

address: 1432-1, Horinouchi

institute: Tokyo University of Farmacy and Life Science

summary: To investigate the alteration of gene expression in IMS32cell under 5 or 15 mM glucose in the presence or absence of 1 mM pyruvate conditions, we conduced microarray analysis.

overall_design: IMS32 cells were incubated for 1 h in DMEM/5%FBS with 5 or 15 mM glucose in the presence or absence of 1 mM pyruvate.

first: Yasumasa

last: Nishito

first: Kazunori

last: Sango


title: Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [ATAC-seq]

first: Linna

last: Peng

first: Shibin

last: Hu

first: Zhenning

last: Wang

first: Aixia

first: Fei

last: Chen


title: Characterization of morphological alterations in micropapillary adenocarcinoma of the lung

first: Dai

last: Sonoda

institute: Kitasato University School of Medicine

summary: Micropapillary adenocarcinoma of the lung is a cancer with poor prognosis and characterized by the presence of tumor cells with ring-like glandular structure floating within alveolar spaces. We investigated the association between its morphological, biochemical, and immunohistochemical characteristics and malignancy using the KU-Lu-MPPt3 cell line established from a patient with micropapillary adenocarcinoma. Two subpopulations of KU-Lu-MPPt3 cells, adhesive (AD) and clumpy and suspended (CS) cells, were prepared and subjected to DNA microarray.

overall_design: Microarray analysis was performed to investigate the changes in gene expression due to morphological differences in KU-Lu-MPPt3 adhesive (AD) cells and KU-Lu-MPPt3 clumpy and suspended (CS) cells established from the micropapillary adenocarcinoma of the lung. In addition, PC9 which is lung adenocarcinoma cell line was added to the sample.

first: Yukiko

last: Matsuo

first: Masashi

last: Mikubo

first: Yukitoshi

last: Satoh


title: Hypoxia PET Imaging Identifies Immunosuppressive Tumor Microenvironments and Guides Targeted Evofosfamide Therapy to Rescue Checkpoint Blockade Refractory Tumors

city: Birmingham

first: Benjamin

last: Larimer

state: AL

address: 1824 6th AVE S, WTI 399S

department: Radiology

institute: University of Alabama at Birmingham

summary: The results generated from this work provide an immediately translatable paradigm for measuring and targeting hypoxia to increase response to immune checkpoint therapy and using hypoxia imaging to guide combinatory therapies.

overall_design: probed the tumor and its surrounding microenvironment with 18F-FMISO PET imaging to non-invasively quantify tumor hypoxia in vivo prior to and during PD-1 and CTLA-4 checkpoint blockade in preclinical models of breast and colon cancer.

first: Kirsten

last: Reeves


title: Transcriptome Analysis by RNA-Seq Defining the Immunomodulatory Activities of PW in THP-1 Derived Macrophages

city: Tianjin

first: Rui

address: No. 22, Meteorological Station Road, Heping District, Tianjin

institute: Tianjin Medical Univercity

summary: To better define the pro-inflammatory and anti-inflammatory activity of PW,the high-throughput RNA-Seq analysis was conducted to obtain the transcriptomic profiles of PW treatment on the macrophages in the absence and presence of the LPS stimulation

overall_design: 12 samples of THP-1 derived macrophages  RNA-Seq profiles,control group and treatment group(hybrids-PW, TLR ligands LPS or both the hybrid-PW and TLR ligands LPS stimulus) each group had three replicates.

first: Hong

last: Yang

first: Shan-Yu

last: Fung


title: Ribosome profiling data of HEK293T cells treated with C13-benzamidyl cycloheximide

city: Cambridge

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

institute: Harvard University

summary: We performed ribosome profiling in HEK293T cells with treatment with either C13-benzamidyl cycloheximide (hereafter "benzamide") or cycloheximide.

overall_design: In order to evaluate the effect that the benzamide has on genome-wide ribosome occupancy, we performed ribosome profiling in duplicate and compared 1-minute pretreatment with 350 μM benzamide or with 350 μM cycloheximide.

middle: B

first: Yongho

last: Park

first: Yumi

last: Koga


title: AC-motif: A DNA motif containing adenine and cytosine repeat plays a role in gene regulation

city: Suwon-si

first: Jeong Hwan

last: Hur

state: No State

address: 2066, Seobu-ro, Jangan-gu, Rm 6317

country: South Korea

institute: Sungkyunkwan University

summary: We confirmed that this new DNA motif present in the gene promoter region has a functional role in gene regulation using genome edited mutant cell lines.

overall_design: Magnesium-containing media was substituted after 24 hrs, and cultured another 24 hrs at 37oC. Cells were collected and washed with PBS

first: Jeong

middle: H

first: Kyeong

last: Kim

first: Chan

middle: Y

last: Kang

first: Nazia

last: Parveen

first: Jihyeon

last: Yu

first: Amen

last: Shamim

first: Sangsu

last: Bae


title: Effects of the Combination Therapy of a CDK4/6 and a MEK inhibitor in a Mouse Model of Diffuse Midline Glioma

city: Chicago

first: Yusuke

last: Tomita

state: Illinois

address: 225 E Chicago Ave Box 18

department: Pediatrics

institute: Northwestern University

summary: Diffuse intrinsic pontine glioma (DIPG) arises in the brainstem of children, leading tumor-related death among children. A heterozygous histone H3.3K27M mutation has been shown to occur in ~80% of DIPGs, and results in brainstem gliomagenesis. There is no clinical trial for the patients with DIPG that proved to prolong survival time so far. Recently, CDK4/6 inhibitor showed feasibility and early therapeutic effect against DIPG. Also, recent research with human DIPG specimens have detected the MAPK pathway highly activated. Here, we evaluated a novel combination therapy with CDK4/6 inhibitor and MEK inhibitor to the mouse DIPG model.  In order to generate DIPG‐bearing mice, we are using the RCAS/Tv‐a system, with which we are able to target specific genetic alterations in RCAS viruses (avian retroviruses) to specific cells‐of‐origin using transgenic Tv‐a‐expressing mice (Tv‐a being the receptor for RCAS viruses). We injected P3‐P5 Nestin-Tv-a;p53fl/fl mice (C56Bl/6 background) with RCAS‐PDGF‐A + RCAS‐H3.3K27M, and RCAS-Cre. The mice are treated with vehicle (methylcellurose), ribociclib as monotherapy, trametinib as monotherapy, and ribociclib and combination as combination. For short-term use, tumor tissues treated with ribociclib showed cytostatic effect, and those treated with trametinib showed cytotoxic effect, and those with combination showed both. Long-term use showed that combination therapy modestly prolonged mice survival compared with vehicle. Therefore, we need to find how DIPG showed registence to the long-term chemotherapy.

overall_design: Examination of gene expression differences in mouse DIPGs treated with vehicle, ribociclib, trametinib, and ribociclib and trametinib as combination

first: Oren

middle: J

last: Becher


title: Transcriptome response of lung in response to vaccination of inactivated whole cells of A. baumannii

city: Chengdu

first: Yun

last: Shi

address: No 37, Guoxuexiang

institute: West China Hospital, Sichuan University

summary: We apply RNAseq of lung tissues to study the innate immune response to vaccination of inactivated whole cells of A. baumanni.

overall_design: Rag1-/- mice were immunized intranasally with A. baumannii IWC and then challenged with a lethal dose of A. baumannii at day 7 after immunization. Lung samples were collected from  control mice, mice immunized with IWC at day 2,  day 7 after immunization with IWC,  A. baumanni infected mice at 24 hours post infection and IWC immunized mice at 7 day after A. baumannii challenge at 24 hours post infection.

first: Hao

last: Gu


title: Transcriptome, proteome, and metabolome of lens fiber cells from mice exposed to cigarette smoke

city: Baltimore

first: S. Amer

last: Riazuddin

address: 600 N. Wolfe street

institute: Johns Hopkins University

summary: We adopted an omics (transcriptome, proteome, and metabolome) approach to characterize the differentially regulated molecules in mouse lens fiber cells exposed to cigarette smoke (CS). Eight pregnant female mice (gestation days 19-20) were placed in a smoking chamber that served as a CS-exposed group. The mothers and newborn pups were exposed to CS for five hours/day, five days/week for 110 days. In parallel, mice were kept in normal cages that served as a control group. The ocular lenses were isolated and fiber cells were separated from the lens epithelium under a microscope. The control and CS-exposed groups were maintained in four biological replicates each consisting of a pool of lens fiber cells from four eyes. The eight biological replicates (four control and four CS-exposed) of fiber cells were used for the next-generation-based transcriptome (RNA-Seq) sequencing, mass-spectrometry-based proteome, and metabolome profiling. RNA-Seq analysis identified the expression (≥1.0 FPKM) of 9,590 and 9,531 genes in control and CS-exposed fiber cells, respectively. The analysis identified 348 differentially expressed genes, which included 186 downregulated and 162 upregulated genes in CS-exposed fiber cells. Proteome profiling revealed a total of 2,424 proteins in control and CS-exposed fiber cells. Metabolome profiling identified a total of 280 metabolites, marked with decreased levels of branched-chain amino acids (BCAAs)-related metabolites in CS-exposed fiber cells. In conclusion, we have established a comprehensive omics profile of CS-exposed lens fiber cells. To the best of our knowledge, this is the first report investigating a comprehensive omics profile of CS-exposed fiber cells.

overall_design: Next-generation (NG)-based whole transcriptome sequencing (RNA-Seq) was performed for lens fiber cells isolated from control (CT-FC) and cigarette smoke (CS-FC) exposed mouse eyes. Total RNA was subjected to RNA-Seq library preparation using NEB Next Ultra RNA Library Prep Kit. Eight RNA-Seq bar-coded pooled libraries were sequenced (2 × 150 bp) on a HiSeq 2500. The raw reads (FASTQ) were processed and analyzed using combinations of algorithms (STAR, HTSeq, and DESeq2). The paired-end reads were aligned to the Mus musculus genome (GRCm38/mm10) using the STAR algorithm (Ver. 2.5). The HTSeq (Ver. 0.6.1) was used for the quantification of gene expression using mapped reads. The expression data were normalized by calculating the fragment per kilobase per million mapped reads (FPKM) values for each gene.  Differential gene expression analysis was performed using the DESeq2.

first: Shahid

last: Khan

first: S


title: Identification of Exosomal microRNA signature by liquid biopsy in Hereditary Hemorrhagic Telangiectasia patients

city: Granada

first: Jordi

last: Martorell-Marugan

address: Avenida de la Ilustración 114

department: Bioinformatics Unit

country: Spain

institute: GENyO

type: Non-coding RNA profiling by high throughput sequencing

summary: Hereditary hemorrhagic telangiectasia (HHT) is a rare autosomal dominant vascular dysplasia characterized by epistaxis, mucocutaneous telangiectases, and arteriovenous malformations (AVM) in visceral organs. In this study, we carried out a liquid biopsy consisting in the isolation of total RNA from plasma exosomes samples from HHT type 1 (HHT1 group) and type 2 (HHT2 group) patients, and healthy relatives (Control group). Upon gene expression data processing and normalization, a bioinformatics analysis was performed for the study of principal components, hierarchical clustering and pairwise comparisons between HHT samples and control group. Results were evaluated in a further validation cohort of HHT and healthy donors by real time PCR and the diagnosis value of exosomal miRNA determined by the ROC curves analysis. We found that exosomal miRNA expression signature clearly distinguishes among healthy and HHT samples and types. Thus, we identified a disease-associated molecular fingerprint of 35 miRNAs over-represented, being 8 specifics for HHT1 and 11 for HHT2; and 30 under-represented, including 9 distinctive for HHT1 and 9 for HHT2. These exosome-transported miRNAs have diagnosis value for HHT, and even allow to distinguish between HHT1 and HHT2.

overall_design: Control group, healthy donors (n=10); HHT1 patients group (n=15); HHT2 patients group (n=15). Each sample was analyzed in triplicates.

first: Ana

last: Pozo-Agundo

first: Nerea

last: Villaescusa

last: Martorell-Marugán

first: Olga

last: Soriano

first: Socorro

last: Leyva

first: Ana-Belén

last: Jódar-Reyes

first: Luisa-María

last: Botella

first: Pedro

last: Carmona-Sáez

first: Francisco-Javier

last: Blanco


title: Stabilization of Pol II protein, orchestration of transcription cycles, and maintenance of enhancer landscape by general transcription regulator SPT5 [ChIP-seq]

city: Shanghai

first: Linna

last: Peng

address: Dong'an Road

institute: Fudan University

summary: Transcription machinery progression is governed by multitasking regulators including SPT5, an evolutionarily conserved factor implicated in virtually all transcriptional steps from enhancer activation to termination. Yet its mechanistic understanding in human cells remains incomplete. Here we utilize rapid degradation system and reveal crucial function of SPT5 in maintaining cellular and chromatin Pol II levels. Rapid SPT5 depletion causes a pronounced reduction of paused Pol II at promoters and enhancers, distinct from NELF degradation resulting in short-distance paused Pol II redistribution. Most of genes exhibit down- but not upregulation, accompanied by greatly impaired transcription activation and altered chromatin landscape at enhancers, and severe Pol II processivity defects at gene bodies. Phosphorylation of KOWx-4/5- linker potentiates pause release and is antagonized by Integrator-PP2A (INTAC) targeting SPT5 and Pol II. Our findings position SPT5 as an essential positive regulator of global transcription by controlling cellular Pol II levels, enhancer activation and landscape, paused Pol II stability, elongation processivity and termination in human.

overall_design: We performed PRO-seq, ATAC-seq, RNA-seq, ChIP-seq, or TT-seq to investigate the role of SPT5 in regulating transcription. In this study, samples for each condition were collected in biological duplicates. Cells were treated with dTAG13 for 3, 12,or 24 hours, the corresponding control cells were treated for the same duration with vehicle only (DMSO) at the same vol/vol dilution.

first: Shibin

last: Hu

first: Zhenning

last: Wang

first: Aixia

last: Song

first: Fei

middle: X

last: Chen


title: Transcriptomic analysis of MSTO-211H cell variant resistant to CAR T cell therapy

city: New york

first: Miguel

last: Lopez-Lago

state: NY

address: 1275 york avenue

department: Surgery

institute: Memorial Sloan-kettering cancer center

summary: We  developed MPM cells from pleural tumors that had relapsed after treatment with M28z CAR T cells

overall_design: We implanted MSTO-211H in the pleura of NSG mice and after 2 weeks we treated mice with CAR T cells. Tumor from mice that relapsed ( 3 mice) were isolated and cells culture in vitro. We generated 3 cell variants from relapsed tumors

first: Prasad

last: Adusumilli


title: mTEChi and mTEClo RNAseq profiling

city: Nantes

first: Matthieu

last: Giraud

address: 30 bd Jean Monnet

department: CRTI

country: France

institute: INSERM _ Université de Nantes

summary: Increased expression of Padi genes in mTEChi

overall_design: Total RNA isolated by Trizol extraction from MHC-II high or low mTECs (from pooled thymi of B6 mice) was used to generate poly-A-selected transcriptome libraries using the non-directionnal TruSeq V3 RNA Sample Prep Kit. Paired-end sequencing (2x100bp) was performed for mTEChi and single-end sequencing (50bp) for mTEClo. Sequencing was done on the Illumina HiSeq2000 machine.

first: Roberto

last: Mallone


title: Transcriptome profile of microRNAs associated with cold tolerance in Dermacentor silvarum ticks

city: Shijiazhuang

first: Desmond

middle: Onyeka

last: Agwunobi

address: No. 20 Road East 2nd Ring South Yuhua District

institute: Hebei Normal University

summary: We identified and functionally explored D. silvarum miRNAs involved in cold response to gain further understanding of the molecular regulatory mechanisms underlying the cold stress in ticks. The microRNA libraries of D. silvarum were established via high-throughput sequencing after exposure to different cold treatments. A total of 147 miRNAs, including 44 known miRNAs and 103 new miRNAs, were identified.

overall_design: Transcriptome profile of adult unfed D. silvarum ticks subjected to cold treatment (8 ℃, 4 ℃, 0 ℃ and -4 ℃) including the control (26 ℃)

first: Tingwei

last: Pei

first: Zhijun

last: Yu


title: Critical conditions for studying Interleukin-11 signalling in vitro and avoid experimental artefacts

city: Singapore

first: Benjamin

last: Ng

address: 8 College Road

country: Singapore

institute: Duke-National University of Singapore Medical School

summary: Interleukin (IL) 11 is upregulated in a number of fibro-inflammatory diseases and cancer, where it binds the cognate IL11 receptor alpha subunit (IL11RA) to form a hexameric IL11:IL11RA:gp130 signalling complex.  Primary cells such as hepatic stellate cells, fibroblasts, and hepatocytes are ideal experimental systems to study IL11 signalling in vitro. In contrast to immortalized cell lines, primary cells better capture physiologically relevant cellular physiology and pathobiology. This collection of protocols details experimental and culturing conditions for primary cells that preserve meaningful cellular states and physiological responses ex vivo in conventional 2D cell culture systems. Our data suggest that cell type, cell culture conditions, passage number, concentrations of stimuli, timing, and other factors have major implications for studies of IL11 signalling. In vitro experiments with primary cell material need to be planned and executed with great caution. Otherwise, physiologically relevant mechanisms may become dysfunctional, and reproducible experimental artefacts can obscure our view of true cytokine biology.

overall_design: RNA-seq of early and late passage human hepatic stellate cells (HSCs: Late, n =4; Early, n=4) and human lung fibroblasts (HLFs, : Late, n =4; Early, n=4).

first: Sivakumar

last: Viswanathan

first: Anissa

last: Widjaja

first: Chee

last: Pua

first: Nevin

last: Tham

first: Jessie

last: Tan

first: Stuart

last: Cook

first: Sebastian

last: Schafer


title: Controlling tissue patterning by translational regulation of signaling transcripts through the core translation factor eIF3c [II]

city: Stanford

first: Gun Woo

last: Byeon

address: 279 Campus Dr., Beckman Center B309

institute: Stanford University

summary: Although gene expression is tightly regulated during embryonic development, the impact of translational control has received less experimental attention. Here, we find that eukaryotic translation initiation factor-3 (eIF3) is required for Shh-mediated tissue patterning.  Analysis of loss-of-function  eIF3 subunit c (Eif3c) mice reveal a unique sensitivity to the Shh receptor Patched 1 (Ptch1) dosage. Genome-wide in vivo enhanced cross-linking immunoprecipitation sequence (eCLIP-seq) shows unexpected specificity for eIF3 binding to a pyrimidine rich motif present in subsets of 5’-UTRs and a corresponding change in the translation of these transcripts by ribosome profiling in Eif3c loss-of-function embryos. We further find that while Eif3c loss-of-function embryos do not show a global decrease in protein synthesis, translation of Ptch1 through this pyrimidine rich motif is specifically sensitive to eIF3 amount. Altogether, this work uncovers hidden specificity of housekeeping translation initiation machinery for the translation of key developmental signaling transcripts.

overall_design: eCLIP-seq

first: Kotaro

last: Fujii

first: Olena

last: Zhulyn

first: Gun

first: Craig

last: Kerr

first: Naomi

last: Genuth

first: Erin

last: Walsh

first: Maria

last: Barna


title: Lysine acetylation restricts mutant IDH2 activity to optimize transformation in AML cells

first: Jing

last: Chen

address: 5801 South Ellis Avenue

institute: The University of Chicago

summary: Mutant isocitrate dehydrogenase (IDH) 1 and 2 play a pathogenic role in cancers including acute myeloid leukemia (AML) by producing oncometabolite 2- hydroxyglutarate (2-HG) . We recently reported that tyrosine phosphorylation activates IDH1 R132H mutant in AML cells. Here we show that, surprisingly, mutant IDH2 (mIDH2) R140Q commonly has K413-acetylation, which negatively regulates mIDH2 activity in human AML cells by attenuating dimerization and blocking binding of substrate (α-ketoglutarate) and cofactor (NADPH). Mechanistically, K413-acetylation of mitochondrial mIDH2 is achieved through a series of hierarchical phosphorylation events mediated by tyrosine kinase FLT3, which phosphorylates mIDH2 to recruit upstream mitochondrial acetyltransferase ACAT1 and simultaneously activates ACAT1 and inhibits upstream mitochondrial deacetylase SIRT3 through tyrosine- phosphorylation. Moreover, we found that the intrinsic enzyme activity of mIDH2 is much higher than mIDH1, thus the inhibitory K413-acetylation optimizes leukemogenic ability of mIDH2 in AML cells by both producing sufficient 2-HG for transformation and avoiding cytotoxic accumulation of intracellular 2-HG.

overall_design: In order to determine whether increased 2-HG level alone is responsible for the elevated cytotoxicity, we treated FLT3 ITD-expressing MOLM14 AML cells with increasing concentrations (100, 250, 500 and 1,000μM) of cell permeable TFMB-2-HG

first: Dong

first: Lei

last: Dong


title: Transcriptomic analysis of NF2 deficient AB12 cells

first: Miguel

last: Lopez-Lago

summary: We  developed Ab12 cells with reduced levels of Nf2 by usin shRNA

overall_design: We compared the transcriptome of AB12 shSC vs AB12 shNF2

first: Prasad

last: Adusumilli


title: Distinct contributions of KAT2A histone acetyl-transferase complexes to human erythropoiesis

first: Cristina

last: Pina

address: Long Road

department: Department of Haematology Cambridge Biomedical Campus NHS - Blood and Transplant

country: United Kingdom

institute: University of Cambridge

summary: KAT2A is a histone acetyl-transferase involved in stabilization of transcriptional activity through acetylation of lysine residue 9 of Histone 3. Mouse knockout models suggest that Kat2a is dispensable for haematopoietic stem and progenitor cell activity, despite a central role in survival and maintenance of Acute Myekoid Leukaemia cells through block of differentiation. Herein, we investigate KAT2A activity in human cord blood haematopoiesis and identify a specific requirement in the establishment of the erythroid lineage. KAT2A is required for specification and survival of Erythroid-Megakaryocytic progenitors, with regulation of expression of the erythropoietin receptor (EPOR) gene, which participates in lineage commitment, as well as of later effector genes in the platelet and erythroid lineages. Early and late lineage roles can be distinctly attributed to the ATAC and SAGA complexes in which context KAT2A exerts its activity. ATAC is active earlier in erythroid lineage development and mediates MEP specification from HSC, whilst SAGA activity is required post-commitment, including in expression of haemoglobin genes. We thus position KAT2A as a novel regulator of human erythropoiesis and separate early and later effects in lineage development with complex specificity. This has implications for putative therapeutic targeting of KAT2A complexes in leukaemia.

overall_design: 2 independent samples of human multipotent haematopoietic K562 cells cultured in maintenance RPMI 20% FBS medium were collected in log growth phase and used for chromatin immunoprecipitation (ChIP) with human SPT20 and human ZZZ3 immune sera (Krebs et al Mol Cell 2011; 44: 410). 10^7 cells were used per IP.

first: Rashmi

last: Kulkarni


title: Pregnancy-activated fibroblasts of the mouse mammary gland

city: Glasgow

first: Torsten

last: Stein

address: College of MVLS

department: School of Medicine

institute: University of Glasgow

summary: The mouse mammary gland undergoes severe morphological changes during each pregnancy cycle. These are controlled by epithelial as well as stromal factors, including fibroblasts. This project aimed to identify factors that are expressed in mammary fibroblasts during early pregnancy (day3) when the first morphological changes become microscopically visible.

overall_design: Fibroblasts were isolated from three individual 12-13 weeks old mice (2nd, 3rd, and 4th gland) 3 days after plug formation, as well as from three virgin litter-mates as decribed previously (Ibrahim et al., 2017). After RNA isolation and RNA amplification, labelled cDNA was hybridised to Illumina Whole-genome mouse microarrays

first: Ayman

last: Ibrahim

first: Joanna

middle: S

last: Morris


title: Neutrophil Gene expression in Acute-on-chronic liver failure (ACLF), Chronic liver disease (CLD) and Healthy Controls_AIIMSND_Aug2020

city: New Delhi

first: Pragyan

last: Acharya

state: Delhi

address: Sri Aurobindo Marg, Ansari Nagar East

department: Biochemistry

country: India

institute: All India Institute of Medical Sciences

summary: To address the molecular basis of immune-dysfunction  in Acute-on-chronic liver failure (ACLF),  we carried out gene expression profiling of blood derived neutrophil from ACLF, belonging to both sterile inflammatory and sepsis conditions. Peripheral whole blood was subjected to PMN enrichment by double gradient centrifugation, and RNA isolation was done by TRIZOL method, followed by microarray experiment using Agilent one-color platform. We compared the gene expression of these neutrophils with that of Chronic liver disease (CLD) patients and healthy controls (HC) for baseline relative quantification, and found unique set of upregulated and downregulated genes in ACLF. We validated the expression of the most differentially expressed genes by quantitative RT-PCR and also stratified the patients into survivors and non-survivors, sepsis and sterile-inflammation. We found an upregulated 3-gene signature of ELANE-MPO-CD177 to be associated with 28-day mortality, irrespective of presence or absence of sepsis.

overall_design: Total RNA from blood enriched neutrophils was subjected to one-color microarray experiment for the following study groups:  ACLF sepsis (n=6), ACLF sterile inflammation (n=6), CLD (n=6), Healthy controls HC (n=6). Differential gene expression analysis was done for CLD vs HC, ACLF overall (n=12) vs CLD, and ACLF sepsis vs sterile inflammation.

first: Rohini

last: Saha


title: Characterization of RNAs bound by THOC1 or LENG8

first: Feng

last: Liu

address: 600 Yishan Road

department: Department of Otolaryngology-Head and Neck Surgery

institute: Shanghai JiaoTong University Affiliated Sixth People's Hospital

summary: Given that LENG8 is associated with the THO complex and is required for mRNA processing, we went on to identify specific RNAs that bind LENG8 or THOC1. Therefore, we precipitated GFP-tagged THOC1, LENG8 or control GFP and sequenced their associated RNAs, using deep sequencing (RNA immune-precipitation followed by deep sequencing, RIP-Seq). We found that when LENG8 was used as bait, 13,328 transcripts from 5,796 genes, were enriched, whereas THOC1 was associated with 32,542 transcripts from 6,150 genes, and 5,179 transcripts from 2,979 genes were enriched in both

overall_design: RNA profiles of THOC1-GFP or LENG8-GFP immuno-precipitates from Hela cells

first: Zhao

last: Yongxu

first: Wang

last: Xiaoting


title: Distinct contributions of KAT2A histone acetyl-transferase complexes to human erythropoiesis [RNA-seq]

overall_design: 2 individual cord blood samples treated as independent biological replicates were enriched for CD34+ haematopoietic stem cells (HSC) and progenitors by magnetic selection using the StemCell Technologies EasySep system. CD34+ cells from each cord blood sample were transduced with lentiviral vectors (LV) encoding a control non-targeting shRNA or a shRNA directed at KAT2A, as well as reporter GFP gene. Four days after LV transduction, cells were sorted by flow cytometry on the basis of GFP expression, coupled with CD34+ CD38- CD45RA- staining to isolate HSC and multipotent progenitors expressing the shRNA of interest. KAT2A knockdown on the paired samples was confirmed by qRT-PCR prior to library preparation.


title: Urine miRNAs as potential biomarkers for systemic reactions induced by exposure to embedded metal

city: Lexington

first: Yuan

last: Wen

address: 760 Press Ave

institute: University of Kentucky

summary: Many veterans live with military grade heavy metal fragments retained in soft tissue. Retained heavy metal fragments may negatively impact health in various organ systems and can manifest as gastrointestinal, neurocognitive, pulmonary and renal disturbances. As such, a better understanding of the long-term effects of retained metals and identification of biomarkers indicative of detrimental health outcomes would benefit clinical decision making. In this study, we analyzed urine microRNAs from rats with military-relevant pure metals implanted in the gastrocnemius muscle for 1, 3, 6, and 12 months. Our results provide potential tissue targets affected by metal exposure and a list of unique or common urine microRNA biomarkers indicative of exposure to one or more metals, highlighting a complex systemic response.

overall_design: Three month old, male, Sprague-Dawley rats (n=8/group) were surgically implanted with one of eight metals of interest (W, Ni, Co, Fe, Cu, Al, Pb, and DU) or tantalum (Ta); Ta, serves as a surgical procedure control because it has been shown to be completely inert when embedded in skeletal muscle. Urine was collected from each rat using hydrophobic sand, one week before and 1, 3, 6, and 12 months after surgically implanting two metal pellets (1 mm diameter x 2 mm length) into each gastrocnemius muscle. Urine collection lasted two hours per session and if the rat produced little or no urine during a session, collection was repeated the next day and urine samples were combined for the two sessions. RNA sequencing was performed on urine samples from two pre-surgery animals per metal and from three-eight post-surgery animals per time-point per metal depending on limited sample volumes available for RNA isolation, totaling 178 samples.

first: Charlotte

middle: A

last: Peterson

first: John

last: McCarthy


title: The Role of the RNA-binding protein HuR in MPNST growth and metastasis [RIP-chip]

city: Derio

first: Jose

middle: Luis

last: Lavin

state: Bizkaia

address: Parque Tecnológico de Bizkaia Building 502, Floor 0

institute: CIC bioGUNE

summary: Oncogenic gene expression programs are essential for the development and maintenance of the cancer phenotype. An emerging view is that cancer cells can develop a strong addiction to discrete molecular regulators that control these aberrant transcription programs, making these attractive targets for effective and enduring therapies. Here, we identify the RNA-binding protein HuR as a central oncogenic driver for Malignant peripheral nerve sheath tumours (MPNSTs), which are highly aggressive sarcomas that originate from cells of the Schwann cell lineage. These neoplasms are strongly metastatic, resistant to radio-and chemotherapy and are typically fatal with no effective treatment. We find that HuR is highly elevated and binds to a multitude of cancer-associated transcripts in human MPNST samples. HuR inhibition has potent cytostatic and cytotoxic effects on tumour growth, and strongly supresses their metastatic capacity in vivo. Importantly, we find that the profound anti-tumorigenic effects of HuR stems from its unique ability to regulate multiple key oncogenic signals that ultimately converge on highly intricate transcription regulatory networks that coordinate the core biological capabilities of MPNST cells. The exceptional dependency on HuR thus confers a competitive advantage to MPNST cells for their survival, proliferation and dissemination, representing an ideal target that could be exploited for MPNST treatment.

overall_design: Ribonomic profiling of HuR mRNA targets in MPNST

first: Ashwin

last: Woodhoo

middle: L

last: Lavín


title: The Role of the RNA-binding protein HuR in MPNST growth and metastasis

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

overall_design: Refer to individual Series


title: The Role of the RNA-binding protein HuR in MPNST growth and metastasis [RNA-seq]

overall_design: Gene expression changes after HuR silencing in MPNST cell line ST88-14


title: Sequential MAVS- and MyD88/TRIF-signaling triggers anti-viral responses of tick-borne encephalitis virus-infected murine astrocytes

city: Hannover

first: Ulrich

last: Kalinke

state: Lower Saxony

address: Feodor-Lynen-Str. 7

department: Institute for Experimental Infection Research

institute: Twincore, Centre for Experimental and Clinical Infection Research

summary: Upon tick borne encephalitis virus exposure of brain-resident cells, astrocytes are important IFN-β producers that followed a biphasic response, which initially depends on MAVS- and later on MyD88/TRIF-signaling

overall_design: Overall, there are 18 samples of primary astrocytes isolated from two mouse genotypes, C57BL/6 and B6.STOCK-Mavs(tm1Tsc) (MAVS -/-) either PBS treated or infected with tick borne encephalitis virus (TBEV). For each genotype, 3 uninfected, 3 TBEV infected 12 hpi and 3 TBEV infected 24hpi  (3= biological replicates). RNA were extracted from the astrocytes cell lysates and sequenced on Illumina NovaSeq-6000 with 50 bp paired-end reads configuration.

first: Luca

last: Ghita

first: Felix

last: Mulenge

first: Imke

last: Steffen


title: The Role of the RNA-binding protein HuR in MPNST growth and metastasis [ChIP-seq]

overall_design: Transcriptional regulatory network after ChIP-Seq in MPNST after HuR silencing


title: Transcriptomic changes upon the formation of a functional "on demand" degradation network in microglia I

city: Bonn

first: Susanne

last: Schmidt

address: Venusberg-Campus 1

department: Institute of Clin. Chemistry and Clin. Pharmacology

institute: University Hospital Bonn

summary: We report the exchange of alpha-synuclein aggregates from one cell to another and examined transcriptomic changes following protein exchange. By obtaining 12,461 genes from isolated RNA samples, we performed differential expression analysis and generated gene ontology enrichment and network analysis. Differential expression (DE) analysis comparing alpha-synuclein-treated with untreated microglia identified 687 upregulated and 1502 downregulated genes. Upregulated genes were linked to inflammation, apoptosis, ER stress and intracellular protein targeting, while downregulated genes included categories related to mitosis, cytoskeleton and vesicle mediated transport. Co-culturing alpha-synuclein treated with untreated microglia largely suppressed the inflammatory and apoptotic phenotype of microglia thereby rescuing cells from cell death.

overall_design: Examination of transcriptomic changes in primary microglia treated with alpha-synuclein

first: Hannah

last: Scheiblich

first: Cira

last: Dansokho

first: Dilek

last: Mercan

middle: V

first: Luc

last: Bousset

first: Alexandru

last: Odainic

first: Jasper

last: Spitzer

first: Stephanie

last: Schwartz

first: Eicke

last: Latz

first: Ronald

last: Melki

first: Michael

middle: T

last: Heneka


title: Hematopoietic stem cells (HSCs) and multipotent progenitors (MPPs)

status: Public on Sep 27 2021

first: Yan

last: Liu

address: Northwestern University, 303 East Superior Street, Lurie 5-107

institute: Department of Medicine

summary: Transcriptional profiling of hematopoietic stem and progenitor cells comparing Bmi1 KO HSCs and MPPs to WT HSCs and MPPs

overall_design: Two-condition experiment, Bmi1 KO HSCs vs. WT HSCs; Bmi1 KO MPPs vs. WT MPPs. Biological replicates: 3 Bmi1 KO replicates, 3 WT replicates.


title: Cardiac response to thromboxane-prostanoid receptor antagonism in a mouse model of muscular dystrophy

city: Pittsburgh

first: Cristi

middle: Lara

last: Galindo

state: Pennsylvania

address: 200 Lothrop Avenue

institute: University of Pittsburgh

summary: Expression analysis of left ventricle taken from wildtype or delta-sarcoglycan knockout mice, a model of muscular dystrophy. Mice were treated from weaning with vehicle or the thromboxane-prostanoid (TP) receptor antagonist ifetroban. Results provide insight into effects of TP receptor antagonism on cardiomyopathy of muscular dystrophy.

overall_design: 2x2 design (WT/KO, vehicle/drug).

first: Erica

last: Carrier

first: James

last: West


title: Transcriptomic changes upon the formation of a functional "on demand" degradation network in microglia II

summary: We report the exchange of alpha-synuclein aggregates from one cell to another and examined transcriptomic changes following protein exchange. Differential expression (DE) analysis comparing alpha-synuclein-treated with untreated microglia identified alpha-synuclein induceable genes which were linked to inflammation, apoptosis, ER stress and intracellular protein targeting, while downregulated genes included categories related to mitosis, cytoskeleton and vesicle mediated transport. Co-culturing alpha-synuclein treated with untreated microglia largely suppressed the inflammatory and apoptotic phenotype of microglia thereby rescuing cells from cell death. Most importantly, these transprictomic changes were prevented by co-culturing the cells without direct cell-cell contact (transwell).

overall_design: Examination of transcriptomic changes in primary microglia treated with alpha-synuclein and cells that were co-cultured either with or without direct cell-cell contact.

first: Lena

last: Wischhof

first: Frederik

last: Eikens

first: Angelika

last: Griep

first: Daniele

last: Bano


title: Single-cell RNA sequencing identifies macrophage transcriptional heterogeneities in granulomatous diseases

city: Aurora

first: Ivana

last: Yang

state: CO

address: 1635 Aurora Ct

institute: University of Colorado

summary:
Purpose: Using single-cell RNA sequencing to explore the common and unique pathways between progressive (SarcP) and remitting (SarcR) sarcoidosis as well as chronic beryllium disease (CBD) and sarcoidosis, focusing on macrophages and macrophages subpopulations (recruited vs. resident).
Methods: We used scRNA-seq to analyze BAL cells from SarcP (N=2), SarcR (N=2), and CBD (N=3) compared to beryllium sensitized non-diseased subjects (BeS; N=2) or healthy control (Con; N=4). The controls were from Mould KJ, et al. Airspace Macrophages and Monocytes Exist in Transcriptionally Distinct Subsets in Healthy Adults. Am J Respir Crit Care Med 2020. We used the R package Seurat to project cells unto Uniform Manifold Approximation and Projection (UMAP) 2D space, identify cell clusters, and detect differentially expressed (DE) genes.
Results: We focused our analysis on macrophages (excluding cell clusters going through the cell cycle). We first compared disease groups to healthy control Using False Discovery Rate (FDR) adjusted p<0.05 and absolute log fold change (log FC)>0.25. We identified 191, 242, and 234 DE genes within all macrophages for the comparisons of SarcP vs. Con, SarcR vs. Con, and CBD vs. Con, respectively, with 82 genes common to all three comparisons; 47 out of the 82 genes were common to all comparisons in regards to recruited macrophages.
Conclusions: We focused this first single-cell transcriptome study in granulomatous lung disease on macrophages. This study offers investigators cell-specific transcriptional changes (genes and networks/pathways) to consider mechanisms of granulomatous disease and as potential drug targets.

overall_design:
Single-cell RNA-seq for granulomatous disease.

**Submitter declares that the raw data were not submitted due to patient privacy concerns**

first: Shu

last: Liao


title: The effect of over expression of StZFP2 on the wound response in Arabidopsis

city: Beltsville

first: Jonathan

last: Shao

state: MD

address: 10300 Baltimore Ave.

department: ARS

institute: USDA-ARS-Beltsville

summary: Expression of genes in Arabidopsis Col-0 and 2 lines of overexpressing StZFP2 (OEEV47 1 and 2) were harvested without wounding (control) and 1h and 6h after wounding

overall_design: There are 3 replicates for each time point and genotype Col-0 control (A, B,C) OEEV471 (A,B,C) OEEV472 (A, B, C) Wounded 1h Control (A,B,C) OEEV471 A, B, C; OEEV472 (A, B, C) wounded 6h etc

first: Susan

middle: D

last: Lawrence


title: Multiple regression analysis of a comprehensive transcriptomic data assembly elucidates mechanically- and biochemically-driven responses to focused ultrasound blood-brain barrier disruption - additional non-FUS controls

city: Charlottesville

first: Alexander

last: Mathew

state: VA

address: 415 Lane Road

institute: University of Virginia

summary: Focused ultrasound (FUS) blood brain barrier disruption (BBBD) permits the noninvasive, targeted, and repeatable delivery of drugs to the brain. FUS BBBD also elicits secondary responses capable of augmenting immunotherapies, clearing amyloid-β and hyperphosphorylated tau, and driving neurogenesis. Leveraging these secondary effects will benefit from an understanding of how they correlate to the magnitude of FUS BBBD and are differentially affected by the mechanical and biochemical stimuli imparted during FUS BBBD. Microbubble activation (MBA) and contrast enhancement (CE) differentially predicted expression of 1,124 genes 6 h or 24 h later. While there existed overlap in the transcripts correlated with MBA vs CE, MBA was principally predictive of expression of genes associated with endothelial reactivity while CE chiefly predicted sterile inflammation gene sets. Over-representation analysis identified transcripts not previously linked to BBBD, including actin filament organization, which is likely important for BBB recovery. Transcripts and pathways associated with neurogenesis, microglial activation, and amyloid-β clearance were significantly correlated to BBBD metrics. This submission includes non-FUS controls to supplement other studies analyzed within the work (GSE152171, GSE141728).

overall_design: We aggregated 75 murine transcriptomes in a multiple regression framework to identify genes expressed in proportion to biochemical (i.e. contrast MR image enhancement (CE)) or mechanical (i.e. harmonic acoustic emissions from MB-activation (MBA)) stimuli associated with FUS BBBD. Models were constructed to control for potential confounders, such as sex, anesthesia, and sequencing batch. This upload includes controls unused in previous work (GSE152171, GSE141728) but utilized in the correlation analysis described herein.

first: Catherine

middle: M

last: Gorick

first: Richard

last: Price


title: Targeting circRNA TFRC in bladder cancer alleviates urinary tract infections by reducing erythroid progenitor cells

city: Shen Zhen

first: Kang

last: Wu

state: Guang Dong

address: 47 Youyi Road, Luohu District

department: Urology

institute: The Third Affiliated Hospital of Shenzhen University (LuoHu Hospital Group)

summary: the same population of EPCs was detected in bladder cancer patients. The EPCs, whose function could be reversed via anti-CD71 treatment, were induced by the circRNA TFRC (circular RNA derived from the transferrin receptor mRNA; cTFRC) in bladder cancer exosomes.

overall_design: severe immune deficiency in the context of Pseudomonas aeruginosa infection in the urethra of treatment-naïve bladder cancer-bearing mice.

first: Song