title: Expression data of Gr-MDSCs under different treatment

city: Notre Dame

first: Xin

last: Lu

state: IN

address: 100 Mason Center, Building GALVIN Department of Biological Sciences

institute: University of Notre Dame

summary:
Myeloid derived suppressor cells (MDSCs) are a heterogeneous population of immature myeloid cells with differentiation program partially blocked in pathological conditions such as cancer. Through inhibition of T cells especially cytotoxic T lymphocytes (CTLs), MDSCs play important tumor-promoting roles and maintain a state of immunological anergy and tolerance
We used microarrays to profile gene expression of Gr-MDSC and identified differentially altered genes under different drug treatment.

overall_design: For 8-12 weeks old PB-Cre+ PtenL/L p53L/L Smad4L/L mTmGL/+ LSL-LucL/+ (CPPSML) male mice, once the prostate tumor reached 150mm3, the mice were surgically castrated and switched to enzalutamide-admixed diet for 4 weeks. The mice were then euthanized for isolating Gr-MDSCs from prostate tumors. Gr-MDSCs were then seeded into well-plate and treated with Dactolisib, Dasatinib or MDSC as control. RNA was isolated after 6h treatment and prepared for microarray.

first: Lu

last: Xin

first: Liu

last: Guoqiang


title: De novo methylaton of the unmethylated K. phaffii genome by human DNA methyltransferases (DNMTs) [RNA-seq]

status: Public on Feb 28 2020

city: Urbana

first: Jun

middle: S

last: Song

email: songj@illinois.edu, jssong137@gmail.com

state: IL

address: 1110 West Green Street, MC 704

country: USA

institute: University of Illinois, Urbana-Champaign

type: Expression profiling by high throughput sequencing

summary: We engineered combinatorial knock-in of human DNMTs in Komagataella phaffii, a yeast species lacking endogenous DNA methylation, to characterize methylation preferences and functional consequences of individual de-novo DNMTs as well as their combinations.  Methylation preferences were determined through whole-genome bisulfite sequencing (WGBS) experiments. Effects of knock-in on gene expression were determined by RNA-seq. Measurements of genome-wide methylation produced by distinct de-novo DNMTs permitted determination of methylation preferences and aversions specific to individual DNMTs. Combining methylation and gene expression data provided insight about cellular response to the stress of DNA methylation and about the association between gene methylation patterns and changes in transcriptional output.

overall_design: RNA-seq for 13 experimental conditions. Five of these conditions were single gene knock-ins of DNMT1A, DNMT3A1, DNMT3A2, DNMT3B1,or DNMT3L. Three conditions were double knock-ins of DNMT1A and DNMT3L, DNMT3A1 and DNMT3L, or DNMT3A2 and DNMTL. For each of these conditions as well as for the control condition, RNA-seq was performed on total RNA extracted from K. phaffii cells 5 days after generating and validating knock-in strains. The remaining conditions composed a time-course experiment for the double knock-in of DNMT3B1 and DNMT3L in which RNA-seq was performed on total RNA extracted 1, 2, 3, and 4 days after generating and validating knock-in strains. All experiments were performed as biological triplicates. We used fragments per kilobase of transcript per million mapped reads (FPKM) normalization to obtain a table of library-size normalized expression values for each gene in each sample.

first: Pablo

last: Perez-Pinera


title: RNA-Seq of Day 6 in vitro generated cells with and without Mdr1 expression and Elacridar treatment

city: Jupiter

first: Mark

last: Sundrud

state: FL

address: 120 Scripps Way

department: Immunology and Microbiology

institute: The Scripps Research Institute

summary: Multidrug resistance (MDR)-1 acts as a chemotherapeutic drug efflux pump in tumor cells, although its physiologic functions remain enigmatic. Using a recently-developed MDR1-knockin reporter allele (Abcb1aAME/+), we found that constitutive MDR1 expression amongst hematopoietic cells was observed mainly in cytolytic lymphocytes—including CD8+ cytotoxic T lymphocytes (CTL) and natural killer cells—and regulated by Runt-related (Runx) transcription factors. Although MDR1 was dispensable for naïve CD8+ T cell development, it was required for both normal accumulation of effector CTL following acute viral infection and protective function of memory CTL upon challenge with an intracellular bacterium. MDR1 acted early after naïve CD8+ T cell activation to suppress oxidative stress, enforce survival and safeguard mitochondrial function in developing CTL. Together, these data highlight an important endogenous function of MDR1 in cell-mediated immune responses, and suggest that ongoing efforts to intentionally inhibit MDR1 in cancer patients could be counter-productive.

overall_design: 12 total samples, triplicates of 4 samples

first: M

last: Chen

first: A

middle: J

last: Getzler


title: Physiologic expression and function of the MDR1 transporter in cytotoxic T lymphocytes

status: Public on Feb 27 2020

summary:
Multidrug resistance (MDR)-1 acts as a chemotherapeutic drug efflux pump in tumor cells, although its physiologic functions remain enigmatic. Using a recently-developed MDR1-knockin reporter allele (Abcb1aAME/+), we found that constitutive MDR1 expression amongst hematopoietic cells was observed mainly in cytolytic lymphocytes—including CD8+ cytotoxic T lymphocytes (CTL) and natural killer cells—and regulated by Runt-related (Runx) transcription factors. Although MDR1 was dispensable for naïve CD8+ T cell development, it was required for both normal accumulation of effector CTL following acute viral infection and protective function of memory CTL upon challenge with an intracellular bacterium. MDR1 acted early after naïve CD8+ T cell activation to suppress oxidative stress, enforce survival and safeguard mitochondrial function in developing CTL. Together, these data highlight an important endogenous function of MDR1 in cell-mediated immune responses, and suggest that ongoing efforts to intentionally inhibit MDR1 in cancer patients could be counter-productive.
This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: microRNA expression profiles in the esophagus of children with caustic stenosis: a pathway towards esophageal cancer?

city: Botucatu

first: Tainara

middle: Francini

last: Felix

state: SP

address: Av. Prof. Mário Rubens Guimarães Montenegro, s/n, s/n

department: Surgery and Orthopedics

country: Brazil

institute: UNESP

summary:
Study Design: This study aimed to identify global microRNA (miRNA) expression changes in esophageal mucosa cells from children with caustic stenosis, divided into two groups according to the time elapsed after injury (Groups A and B, less and more than five years, respectively), compared with normal esophageal tissues from same patients. miRNA expression profiles were determined using TaqMan Human MicroRNA Arrays (Thermo Fisher). Bioinformatic algorithms were applied to identify miRNA target genes and biological pathways.
Results: Thirteen miRNAs were significantly deregulated (9 over- and 4 under-expressed) in patients from Group A. In patients from Group B, two miRNAs were over- and two were under-expressed. Of note, miR-374 and miR-574 were deregulated in Group B patients and have been linked to esophageal cancer development. We identified signal transduction and transcription factor networks with genes strongly related to esophageal tumorigenesis. Conclusion:There is no literature regarding miRNA expression changes following caustic ingestion in children. miRNAs identified here may help clarify the pathway of malignant transformation from caustic stenosis to esophageal cancer and could lead to the development of novel biomarkers of malignant progression.

overall_design: Group A consisted of samples from children with less than five years of follow-up after caustic injury, and Group B included samples from patients with more than five years of follow-up after injury. Samples from a total of 15 patients were obtained. These samples were paired by age, gender, and year of biopsy with macroscopically and histopathologically normal esophageal tissues (Control - Reference Samples). Samples were pooled to obtain an adequate amount of RNA suitable for miRNA profiling analysis.  Pools are identified in the datasheet.

first: Wilson

middle: E

last: de Oliveira Junior

middle: F

first: Grazielle

last: do Vale Pires

first: Marco

middle: L

last: Lapa

first: Fábio

last: Severino

first: Simone

middle: A

last: Terra

first: Pedro

last: Toledo de Arruda Lourenção

first: Patricia

middle: P

last: dos Reis

first: Erika

middle: V

last: Paiva Ortolan


title: Comprehensive genomic profiling of undifferentiated embryonic sarcoma of the liver

city: Tampa

first: Andrew

middle: Scott

last: Brohl

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

summary: We performed comprehensive molecular profiling on samples from 14 patients diagnosed with UESL

overall_design: including with this submission is CytoScanHD SNP arrays from 13 UESL tumors


title: GATA3 mutation disrupts functional network governed by Estrogen receptor, FOXA1 and GATA3

city: Research Triangle Park

first: Paul

last: Wade

state: NC

address: 111 TW Alexander Drive

department: Laboratory of Molecular Carcinogenesis

institute: NIEHS

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Estrogen Receptor (ER) is a steroid hormone receptor that regulates epithelial genes in breast cancer. ER forms a regulatory network with the other transcription factors, FOXA1 and GATA3. GATA3 is known to be capable of specifying chromatin localization of FOXA1 and ER. GATA3 has been identified as one of the most frequently mutated genes in breast cancer. However, how GATA3 mutations impact this transcriptional network is unknown. Here we investigate the function of one of the recurrent patient-derived GATA3 mutations (R330fs) for this regulatory network. Genomic analysis indicates that the R330fs mutant can disrupt the cooperative action of ER, FOXA1, and GATA3, and induce chromatin relocalization of these factors. Relocalizations of ER and FOXA1 are associated with altered chromatin architectures leading to differential gene expression in the GATA3 mutant cells. These results suggest the active role of GATA3 mutants in ER positive breast tumors.

overall_design: Genome-wide mapping of chromatin architectures in GATA3 mutant T47D cells

first: Motoki

last: Takaku

first: Sara

last: Grimm

first: Wade

last: Paul


title: Gene expression profiling of murine tumors derived from Renca control knockout vs Pbrm1 knockout tumor clones

status: Public on Feb 26 2020

city: Houston

first: Christine

middle: B.

last: Peterson

state: TX

address: 1400 Pressler St.

department: Biostatistics

institute: University of Texas MD Anderson Cancer Center

summary: We investigated the influence of Pbrm1 on the tumor microenvironment in murine tumors. We employed a Renca-BALB/c murine immune competent model for our study. We compared Renca control knockout tumors to two Pbrm1 KO tumor clones (n=5 for each of two clones).

overall_design: RNASeq of Renca control knockout (n=5) and Pbrm1 knockout tumor clones (n=5 for each of two clones)

middle: B

first: Xian-De

last: Liu


title: ATAC-seq identifies accessible chromatin domains in gastrula stage Xenopus laevis

city: Philadelphia

first: Peter

last: Klein

state: PA

address: 3400 Civic Center Blvd

department: Medicine

institute: University of Pennsylvania School of Medicine

summary: In the embryo, inductive cues are interpreted by competent tissues in a spatially and temporally restricted manner, and the mechanisms for the loss of responsiveness are not well understood. To test the hypothesis that loss of competence is associated with changes in chromatin accessibility, we adapted the assay for transposase-accessible chromatin with high throughput sequencing (ATAC-seq) for use in Xenopus laevis to evaluate genome-wide changes in chromatin accessibility in early and late gastrula stages. ATAC-seq was performed on presumptive ectoderm (animal caps) explanted at the blastula stage and cultured until siblings reached early (stage 10) or late (stage 12) gastrula stage. Approximately 70,000 accessible regions were identified at intergenic regions, introns, promoters, and transcription termination sites at both stages. Accessibility decreased from stage 10 to stage 12 at 279 promoters, including developmental regulators such as Foxh1, chordin, and VegT. Accessible chromatin domains overlap extensively with previously reported p300 binding sites, consistent with putative cis-regulatory modules (pCRMs), and these pCRMs are enriched for binding motifs for pluripotency factors, including Sox, Oct/Pou, and KLF binding motifs. Dorsal Wnt target gene promoters are not accessible after the loss of competence, but inhibition of histone deacetylases increases acetylation at these promoters and extends competence for dorsal gene induction by Wnt signaling. In contrast, the promoters for genes involved in mesoderm and neural crest development remain open through gastrulation, and histone deacetylase inhibition does not extend competence for mesoderm or neural crest induction. These data suggest that chromatin state regulates the loss of competence to inductive signals in a context-dependent manner.

overall_design: ATAC-seq performed on ectodermal explants from stage 10 (early gastrula) and stage 12 (late gastrula).

first: Jing

last: Yang

first: Kai

last: Zhang

first: Melody

last: Esmaeili


title: Characterization of gene expression patterns among PXB-cells, cryopreserved primary human hepatocytes, HepaRG cells, HepG2 cells, and total human liver tissue

city: Fujisawa

first: Tadahiro

last: Shinozawa

address: Muraokahigashi 2chome

country: Japan

institute: Takeda pharmaceuticals

summary: Here we provide the gene expression patterns of PXB-cells , primary human hepatocytes (PHH), and HepaRG cells in Matrigel sandwich culture, HepG2 cells in 2D culture, and total human liver tissues. These data will provide insight into the appropriate selection of the cells for in vitro cellular models.

overall_design: Comparison of transcriptome profiling among multiple hepatic tissues and cells including  PXB-cells, cryopreserved PHHs, HepaRG cells, HepG2 cells, and total human liver tissue.

first: Hiroshi

last: Kohara

first: Akimitsu

last: Miyawaki


title: Pooled CRISPR screens in human intestinal organoids [CUT&RUN]

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

summary: We performed CRISPR screens on both a sub-library and a genome-wide scale in human intestinal organoids to discover cancer driver genes. We investigated the Wnt and the TGFB pathway and used both WT, APC-mutant and APC-TP53-mutant organoids.

overall_design: To investigate how the identified SWI/SNF screening hits confer TGFB resistance, we assessed changes in binding of SMAD3 to the chromatin upon ARID1A or SMARCA4 perturbation and TGFB treatment

first: Till

last: Ringel

first: Nina

last: Frey

first: Femke

last: Ringnalda

first: Sharan

last: Janjuah

first: Sarah

last: Cherkaoui

first: Stefan

last: Butz

first: Sumana

last: Srivatsa

first: Martin

last: Pirkl

first: Giancarlo

last: Russo

first: Lukas

last: Villiger

first: Gerhard

last: Rogler

first: Hans

last: Clevers

first: Niko

last: Beerenwinkel

first: Nicola

last: Zamboni

first: Tuncay

last: Baubec

first: Gerald

last: Schwank


title: Developmentally regulated requirement for the conserved transcription factor Grainy head in determining chromatin accessibility

city: Madison

first: Melissa

middle: M

last: Harrison

email: mharrison3@wisc.edu, ykaur@wisc.edu, torreszelada@wisc.edu, mmfreund2@wisc.edu

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

summary: Pioneer transcription factors initiate changes in gene expression by binding to cis-regulatory modules and promoting chromatin accessibility. It is suggested that this activity is an essential first step in priming these sites for the binding of other factors. Nonetheless, it is unclear whether pioneering activity is always required when these factors are present during development. The highly conserved, essential transcription factor Grainy head was recently identified as a pioneer factor in Drosophila larval imaginal discs, yet Grainy head is present throughout development. To determine whether Grainy head maintains its pioneering role throughout development, we performed ATAC-seq on embryos lacking either maternal or zygotic Grainy head at three stages of development (stage 5, stage 6, and stage 15). Surprisingly, we discovered that neither maternal nor zygotic Grainy head are required for chromatin accessibility in early embryogenesis. Nonetheless, we find that Grainy head binding is correlated with some cis-regulatory modules that gain chromatin accessibility at gastrulation. Intriguingly, later in embryogenesis Grainy head gains a role in promoting chromatin accessibility. Additionally, we determined that Grainy head is able to remain bound to mitotic chromatin, like other pioneer factors, yet this ability is separate from its pioneering activity. Our data reveal that Grainy head pioneering activity is temporally, suggesting that other unidentified pioneer factors compensate for the loss of Grainy head.

overall_design:
ATAC-seq chromatin accessibility profiling of Drosophila melanogaster embryos either wild-type or lacking maternal or zygotically expressed Grainy head at embryonic stages 5, 6, and 15
Please note that each narrowpeak data file was generated from all replicates and is linked to the corresponding rep1 sample records.

first: Markus

last: Nevil

first: Tyler

last: Gibson

first: Constantine

last: Bartolutti

first: Anusha

last: Iyengar


title: Transcriptomic analysis of BAP1 negative primary and metastatic uveal melanoma tumors

city: Liverpool

first: Carlos

middle: Rogerio

last: De Figueiredo

state: Merseyside

address: 6 West Derby Street

department: Molecular and Clinical Cancer Medicine

country: United Kingdom

institute: University of Liverpool

summary: Individualized immune transcriptome analysis were successfully constructed through expression profiling of a total of immune genes in uveal melanoma tumors.

overall_design: In the study presented here, a cohort of 4 primary Uvea Melanoma (pUM) tumors and 6 metastatic Uveal Melanoma tumors (mUM) all with loss of BAP1 expression were used to acquire expression profiles of a total of 737 immune genes leading to the successful correlation analysis and construction of supervised and unsupervised transcriptome analysis.

middle: R

last: Figueiredo

first: Helen

last: Kalirai

first: Joseph

last: Sacco

first: Ricardo

last: Azevedo

first: Andrew

last: Duckworth

last: Slupsky

first: Judy

last: Coulson

first: Sarah

last: Coupland


title: The role of methyl-CpG-binding domain protein-2 (MBD2) in colonic inflammation [series 2]

city: Edinburgh

first: Alasdair

last: Ivens

address: Kings Buildings

institute: Centre for Immunity, Infection and Evolution

summary:
Mice deficient in MBD2 (Mbd2-/-) were treated with 2% dextran sulfate sodium or normal drinking water for 6 continuous days. A single cell suspension of colon lamina propria and epithelium was isolated, with monocytes (CD11b+ Ly6CHi, MHC-II+/-), macrophages (CD11b+ Ly6C-MHC-II+), cDC2s (CD11b- CD11c+ CD103+) and epithelial cells (CD45- EpCAM+) purified by FACS.
Methyl-CpG-binding domain-2 (Mbd2) acts as an epigenetic regulator of gene expression, by linking DNA methylation to repressive chromatin structure.  Although Mbd2 is widely expressed in gastrointestinal immune cells and is implicated in regulating intestinal cancer and anti-helminth responses, its role in controlling colitis has yet to be defined. Indeed, epigenetic control of gene expression in cells that regulate intestinal immunity is generally poorly understood, even though such mechanisms may explain the inability of standard genetic approaches to pinpoint the causes of conditions like inflammatory bowel disease. In this study we demonstrate a vital role for Mbd2 in regulating murine colonic inflammation. Mbd2-/- mice displayed dramatically worse pathology than wild type controls during dextran sulphate sodium (DSS) induced colitis, with increased inflammatory (IL-1β+) monocytes. Profiling of mRNA from innate immune and epithelial cell (EC) populations suggested that Mbd2 suppresses inflammation and pathology via control of innate-epithelial cell crosstalk and T cell recruitment. Consequently, restriction of Mbd2 deficiency to CD11c+ dendritic cells and macrophages, or to ECs, resulted in increased DSS colitis severity.  Our identification of this dual role for Mbd2 in regulating the inflammatory capacity of both CD11c+ cells and ECs highlights how epigenetic control mechanisms may limit intestinal inflammatory responses.

overall_design: 2-5 replicates per group, each replicate made up of 1-5 mice.

middle: C

first: Gareth-Rhys

last: Jones


title: The transcriptomes of PC3 cells with or without KLF16 interference

city: Shanghai

first: Wandong

last: Yu

state: China

address: No. 801, Heqing Road, Minhang District, Shanghai

country: China

institute: The Fifth People’s Hospital of Shanghai, Fudan University

summary: Total RNA was obtained from PC3 cells with or without KLF6 interference to perform a High-throughput sequencing

overall_design: The prostate cancer cell line PC3 expressing shRNA targeting KLF16 or a control sequence. The gene transcript expression profiles were generated by deep sequencing.

first: Jun

last: Zhang

first: Guowei

last: Shi


title: Integrative analysis of lncRNAs, miRNAs, and mRNA-associated ceRNA network in lung tissue of aging mice and changes after intervention of Codonopsis pilosula (miRNA dataset)

city: Lanzhou

first: Dongmei

last: Chen

address: No. 35 Dingxi east road, chengguan district, Lanzhou, Gansu province

institute: Gansu University of Chinese Medicine

summary: Codonopsis pilosula, a kind of traditional Chinese medicine, possesses anti-aging effect. However, the anti-aging effect of Codonopsis pilosula on lung remains largely unknow and the exact molecular mechanism of Codonopsis pilosula anti-aging also needs to be further studied. Thus, we investigated the protective effect of Codonopsis pilosula on aging lung and the exact molecular mechanism of Codonopsis pilosula anti-aging. To test this hypothesis, we established the aging mice model, and then used Codonopsis pilosula to intervene. Microarray analysis and bioinformatics methods were used to comprehensively analyze lncRNA-miRNA-mRNA (ceRNA) network. Our results showed that the aging mice model was established. From the microarray analysis, 138 lncRNAs, 128 mRNAs and seven miRNAs significantly changed after aging, whereas, 282 lncRNAs, 283 mRNAs and 19 miRNAs were dysregulated after intervention of Codonopsis pilosula. KEGG pathway analysis was performed to explore the signaling pathways involved. Compared with the ceRNA network in aging mice and after intervention of Codonopsis pilosula, we found three mRNAs (Hif3a, Zbtb16, Plxna2) and one lncRNA (NONMMUT063872) associated with Codonopsis pilosula anti-aging and they were validated by qRT-PCR. Altogether, our results showed that Codonopsis pilosula has the protective effect on aging lung and the ceRNA network plays an important role in Codonopsis pilosula anti-aging.

overall_design: miRNA was extracted from lung tissues in the control group, the model group and high dose Codonopsis pilosula intervention group (n=3 mice).

first: Jiajia

last: Liu

first: Jie

last: Meng

first: Dandan

last: Li

first: Pan

last: Zhao

first: Yongqiang

last: Duan

first: Li

first: Jing

last: Wang


title: Targeting codon 158 p53-mutant cancers via the induction of p53 acetylation [RNA-seq]

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: Mutations in the DNA binding domain (DBD) of TP53 are often associated with the gain-of-function (GOF) of mutp53, resulting in pervasive transcription of chromatin regulatory genes that promote genome-wide histone methylation and acetylation. Efforts to target this tumor-promoting function of mutp53 remain elusive. Here, we therapeutically exploit the GOF mechanisms of p53 codon 158 mutation, a DBD mutant found to be prevalent in lung squamous cell carcinoma. Using high throughput compound screening and combination analyses, we uncovered that mutp53R158G exhibits strong synergistic cytotoxicity to cisplatin-induced DNA stress and belinostat, a histone deacetylase inhibitor. This treatment regime acetylates mutp53, alters DNA binding motifs and upregulates TRAIP, a RING domain-containing E3 ubiquitin ligase which dephosphorylates IĸB and impedes nuclear translocation of RelA (p65), thus repressing oncogenic nuclear factor kappa-B (NF-ĸB) signalling and inducing apoptosis. This mechanistic intervention was validated with other acetylators of mutp53 and in several cancer models. Given that this transcriptional modulation and cytotoxic vulnerability appears inapt in p53 wild-type (WT) or null cells, our work provides a novel therapeutic opportunity in Arg158 15 -mutp53 tumors utilizing a regimen consisting of DNA-damaging agents and mutp53 acetylators, which is currently being pursued clinically

overall_design: RNA-seq samples of CALU1 lung cancer cell line, of TP53 wild type and mutant, treated and untreated.

last: Kong

first: Tuan

middle: Z


title: The role of methyl-CpG-binding domain protein-2 (MBD2) in colonic inflammation [series 1]


title: Targeting codon 158 p53-mutant cancers via the induction of p53 acetylation

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


title: Mycobacterium tuberculosis associated with severe tuberculosis evades cytosolic surveillance systems and modulates IL-1β production

city: Porto

first: Ana

middle: Raquel

last: Maceiras

address: Rua Alfredo Allen, 208

country: Portugal

summary: Tuberculosis (TB) remains a deadly disease. The genetic diversity of Mycobacterium tuberculosis was neglected in the past, but is increasingly recognized as a determinant of immune responses and clinical outcomes of TB. However, how this bacterial diversity orchestrates immune responses to direct differences in TB severity remains unknown. We studied 681 patients with pulmonary TB and found that phylogenetically related M. tuberculosis isolates from cases with mild disease induced robust cytokine responses in macrophages. In contrast, isolates associated with severe TB cases failed to do so. Using representative isolates, we show that M. tuberculosis inducing a low cytokine response in macrophages also diminished activation of cytosolic surveillance systems, including cGAS and the inflammasome, suggesting a novel mechanism of immune escape. Isolates exhibiting this evasion strategy carried mutations in various components of the ESX-I secretion system. We conclude that host interactions with different M. tuberculosis strains results in variable TB severity.

overall_design: AmpliSeq Transcriptome was performed in bone marrow-derived macrophages infected with two Mtb clinical isolates to compare the induced responses. Non-infected cells were also included as control.


title: The role of methyl-CpG-binding domain protein-2 (MBD2) in colonic inflammation


title: Direct comparison of mononucleated and binucleated cardiomyocytes reveals molecular mechanisms underlying distinct proliferative competencies

first: Michael

middle: Patrick

last: Morley

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: The mammalian heart is incapable of regenerating a sufficient number of cardiomyocytes to ameliorate the loss of contractile muscle after acute myocardial injury, often resulting in heart failure. Several reports have demonstrated that mononucleated (MoNuc) cardiomyocytes are more responsive to pro-proliferative stimuli than are binucleated (BiNuc) cardiomyocytes. However, techniques to isolate and characterize these two different cardiomyocyte populations have been lacking. We have developed a novel fluorescence associated cell sorting method to isolate highly enriched populations of MoNuc and BiNuc cardiomyocytes at various times of development. Transcriptome analysis reveals an underlying biological signature that defines the differences between MoNucs and BiNucs, including a central role for the E2f/Rb transcriptional network in establishing the divergent ability of these two populations to re-enter and complete the cell cycle. Moreover, inducing binucleation by genetically blocking the ability of cardiomyocytes to complete cytokinesis leads to a reduction in E2f target gene expression, linking the E2f pathway with nucleation. These data identify key molecular differences between MoNuc and BiNuc mammalian cardiomyocytes that can be used to leverage cardiomyocyte proliferation for promoting injury repair in the heart.

overall_design: Cardiomyocytes were isolated from Mlc2vcre:R26REYFP mice and sorted by FACS to separate mononucleated and binucleated cardiomyocytes for transcriptome analysis

first: Rebecca

last: Windmueller

first: Micheal

first: Edward

last: Morrisey


title: Genome-wide binding of Arabidopsis growth regulating factors uncovers their broad regulatory functions in plant growth, development and stress response [RNA-Seq]

city: Knoxville

first: Sarbottam

last: Piya

state: Tennessee

address: 2431 Joe Johnson Dr.

department: Plant Science

institute: University of Tennessee

summary:
The goal of this study is to identify genes regulated by GRF1 and GRF3.
Results: 2,596 and 2,212 differentially expressed genes were identified in the 35S:GRF1 and 35S:GRF3 plants, respectively, when compared with the grf1/grf2/grf3 triple mutant  at a false discovery rate (FDR) of 0.05. Similarly, a set of 826 genes was identified as differentially expressed in the grf1/grf2/grf3 mutant when compared with the wild-type WS plants.

first: Tarek

last: Hewezi


title: Effect of HOXB13 overexpression on osteogenic differentiation in mouse embryonic fibroblasts (MEFs)

status: Public on Feb 25 2020

city: los angeles

first: Sandra

last: Orsulic

state: california

address: 10833 Le conte ave

department: OBGYN

institute: UCLA

summary: Studies of the effect of HOXB13 overexpression on mesenchymal stem cell (MSC) marker expression and osteogenic differentiation in mouse embryonic fibroblasts (MEFs)

overall_design: Mouse embryonic fibroblasts (MEFs) from β-actin-TVA/p53−/− mice transduced with RCAS-GFP or RCAS-HOXB13 were cultured in OsteoMAX differentiation media for 21 days and the transcriptome was analysed by RNA sequencing

first: Maria

middle: S

last: Recouvreux

first: Sandram


title: Genome-wide binding of Arabidopsis growth regulating factors uncovers their broad regulatory functions in plant growth, development and stress response [ChIP-Seq]

summary: The goal of this study is to identify direct target of GRF1 and GRF3.

overall_design: 1108 and 2194 peaks were identified for GRF1 and GRF3, respectively


title: Targeting codon 158 p53-mutant cancers via the induction of p53 acetylation [ChIP-seq]

summary: Mutations in the DNA binding domain (DBD) of TP53 are often associated with the gain-of-function (GOF) of mutp53, resulting in pervasive transcription of chromatin regulatory genes that promote genome-wide histone methylation and acetylation. Efforts to target this tumor-promoting function of mutp53 remain elusive. Here, we therapeutically exploit the GOF mechanisms of p53 codon 158 mutation, a DBD mutant found to be prevalent in lung squamous cell carcinoma. Using high throughput compound screening and combination analyses, we uncovered that mutp53R158G exhibits strong synergistic cytotoxicity to cisplatin-induced DNA stress and belinostat, a histone deacetylase inhibitor. This treatment regime acetylates mutp53, alters DNA binding motifs and upregulates TRAIP, a RING domain-containing E3 ubiquitin ligase which dephosphorylates IĸB and impedes nuclear translocation of RelA (p65), thus repressing oncogenic nuclear factor kappa-B (NF-ĸB) signalling and inducing apoptosis. This mechanistic intervention was validated with other acetylators of mutp53 and in several cancer models. Given that this transcriptional modulation and cytotoxic vulnerability appears inapt in p53 wild-type (WT) or null cells, our work provides a novel therapeutic opportunity in Arg158 15 -mutp53 tumors utilizing a regimen consisting of DNA-damaging agents and mutp53 acetylators, which is currently being pursued clinically.

overall_design: ChIP samples of TP53 wild type and mutant, treated and untreated from a cell line were analyzed by next-generation sequencing (Illumina HiSeq 2000).


title: Analysis of gene expression change between ectopic expression SOX2 in T24 bladder cancer cells.

city: Hsinchu

first: Ming-Han

last: Kuo

address: No. 101, Section 2, Kuang-Fu Road, Hsinchu, Taiwan 30013, R.O.C.

country: Taiwan

institute: National Tsing Hua University

summary: We collected total RNA from both T24-Ctrl and T24-SOX2 and examined mRNA expression profile, comprehensively.

overall_design: T24 cells transduced with lentiviral particles encoding HR'-puro (Ctrl) or HR'-SOX2 (SOX2).

first: Y

last: Chiu

first: M


title: Overexpression of subtilate4.13

city: Valencia

first: Eduardo

last: Bueso

state: Valencia

address: Ingeniero Fausto Elio, s/n

department: IBMCP

country: Spain

institute: Universitat Politècnica de València

summary: mutant seedlings overexpressing subtilase4.13 were grown in MS medium during 10 days comparing with wild type

overall_design: three independent replicates of wild type and two overexpressing subtilase4.13 lines were compared. We used seedlings of 10 days old.

first: Jesús

last: Muñoz-Bertomeu

first: Gaetano

last: Bissoli


title: Increased HDAC Activity and c-MYC Expression Mediate Acquired Resistance to WEE1 Inhibition in Acute Leukemia

city: Aurora

first: Etienne

last: Danis

state: CO

institute: University of Colorado, Denver - Anschutz Medical Campus

summary: WEE1 is a cell cycle and DNA damage response kinase that is emerging as a therapeutic target for cancer. AZD1775 is a small molecule inhibitor of WEE1, currently in early phase clinical trials as a single agent and in combination with more conventional anti-neoplastic agents. As resistance to kinase inhibitors is frequent, we sought to identify mechanisms of resistance to WEE1 inhibition in acute leukemia. We found that AZD1775 resistant cell lines are dependent upon increased HDAC activity for their survival, in part due to increased KDM5A activity. In addition, gene expression analyses demonstrate HDAC dependent increase in MYC expression and c-MYC activity in AZD1775 treated resistant cells. Overexpression of c-MYC confers resistance to AZD1775 in cell lines with low base line expression. Pharmacologic inhibition of BRD4, and thereby c-MYC, partially abrogated resistance to AZD1775. Thus, acquired resistance to WEE1 inhibition may be reversed by HDAC or BRD4 inhibition in leukemia cells.

overall_design: AZD1775-sensitive and -resistant Jurkat, Molm13 and REH cells were treated with panobinostat and/or AZD1775 for 24 hr. RNA was isolated, and processed for sequencing using Illumina HiSeq 4000 platform.

first: Tamara

last: Garcia

first: Rajeev

last: Vibhakar

first: Christopher

last: Porter


title: YBEY is an essential biogenesis factor for mitochondrial ribosomes

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

country: Germany

institute: ZB MED - Information Centre for Life Sciences

summary:
Ribosome biogenesis relies on a number of specific factors. Some of them are remarkably conserved, suggesting that they play essential roles even in distant evolutionary contexts. This is namely the case for the UPF0054 protein YBEY found in all bacteria, but also in many Eukarya. Proposed to act as an endoribonuclease processing the 3’ end of 16S rRNA, YBEY is critically required for translation in model bacteria and plant chloroplasts. However, ribosomal RNA processing pathways are poorly conserved between distant phyla, suggesting that YBEY may have another important function in ribosome biogenesis.
We studied the human YBEY homologue and found that it localises in mitochondria. The human mitochondrial rRNAs are flanked by tRNA genes and thereby processed by mitochondrial RNase P and RNase Z, making other ribonucleases superfluous. Yet, CRISPR-mediated knockout of the YBEY gene resulted in a decrease of the mitochondrial small ribosomal subunits (SSU), abolished translation in the organelles and, as a result, led to the inability of the knockout cells to respire. Mapping the ends of the mitochondrial rRNAs revealed no processing defects. Similarly, although human YBEY did show robust RNase activity in vitro and in vivo, mutations in key catalytic residues did not abolish its ability to complement the knockout phenotypes. The analysis of the mitoribosomes identified a distinct set of SSU proteins, mostly located in the head and the platform, to be significantly depleted in the absence of YBEY, including uS11m, required for translation initiation. Importantly, uS11m was the only SSU protein found to directly interact with YBEY in vitro, in vivo and in situ, and forming a stable stoichiometric complex with YBEY. The sum of our data supports the model where YBEY functions primarily as an essential ribosome biogenesis factor by recruiting uS11m in order to complete the assembly of translationally active SSUs.

overall_design: RNA was isolated from mitochondria of three independent YBEY+ and three independent YBEY KO cell lines and analysed by standard RNA-seq.

first: Walter

last: Rossmanith

first: Alexandre

last: Smirnov

first: Akinyemi

last: Fasemore


title: Transcriptomics  revealed the putative mechanism underlying the impact of HFL1 fibroblasts with overexpression of GALC on LoVo cell

city: shanghai

first: Hui

last: Zhao

address: 600 YiShan Road, Shanghai 200233, People's Republic of China.

institute: Shanghai Jiao Tong University

summary:
Purpose:To elucidate the mechanism by which overexpression of GALC senescent fibroblasts promote the tumor properties of LoVo CRC cells
Methods: LoVo cell  which co-cultured with LV-GALC HFL1 fibroblasts cells and LoVo cell which co-cultured with LV-NC HFL1 fibroblasts cells using Transwell chamber were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Conclusions: Our study represents the first detailed analysis of  the impact of LV-GALC HFL1 fibroblasts and LV-NC HFL1 fibroblasts on LoVo cell with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.Fibroblasts regulate the tumorigenicity of CRC cells and play important roles in tumor biology.

overall_design: LoVo mRNA profiles of co-cultured with LV-GALC HFL1 fibroblasts cells and co-cultured with LV-NC HFL1 fibroblasts cells were generated by deep sequencing, in triplicate, using Illumina Illumina HiSeq X Ten.


title: Pooled CRISPR screens in human intestinal organoids

first: giancarlo

last: russo

overall_design: Refer to individual Series


title: Expression data from non-decidualized and decidualized endometrial stromal cell (ESCs) with or  without WT1 knockdown

city: Ube

first: Isao

last: Tamura

address: Minami-Kogushi 1-1-1

department: Department of Obstetrics and Gynecology

institute: Yamaguchi University Graduate School of Medicine

summary:
Wilms tumor 1 (WT1) regulates the expression of insulin-like growth factor-binding protein-1 (IGFBP-1) and prolactin (PRL) during decidualization of human endometrial stromal cells (ESCs).  However, other roles of WT1 in decidualization have not been fully clarified.
We used microarrays to identify the physiological roles of WT1 in the regulation of cellular functions of human ESCs during decidualization.

overall_design: Three types of cells (no treatment with control siRNA, cAMP treatment with control siRNA, and cAMP treatment with WT1 siRNA) were generated for RNA.

first: Norihiro

last: Sugino


title: Dynamic chromatin targeting of BRD4 stimulates cardiac fibroblast activation [RNA-seq]

first: Timothy

last: McKinsey

department: Division of Cardiology

institute: University of Colorado Anschutz Medical Campus

summary: Small molecule inhibitors of the acetyl-histone binding protein BRD4 have been shown to block cardiac fibrosis in pre-clinical models of heart failure (HF). However, the mechanisms by which BRD4 promotes pathological myocardial fibrosis remain unclear. Here, we demonstrate that BRD4 functions as an effector of TGF-b signaling to stimulate conversion of quiescent cardiac fibroblasts into Periostin (Postn)-positive cells that express high levels of extracellular matrix. BRD4 undergoes stimulus-dependent, genome-wide redistribution in cardiac fibroblasts, becoming enriched on a subset of enhancers and super-enhancers, and leading to RNA polymerase II activation and expression of downstream target genes. Employing the SERTA domain-containing protein 4 (Sertad4) locus as a prototype, we demonstrate that dynamic chromatin targeting of BRD4 is controlled, in part, by p38 mitogen-activated protein kinase, and provide evidence of a novel function for Sertad4 in TGF-b-mediated cardiac fibroblast activation. These findings define BRD4 as a central regulator of the pro-fibrotic cell state of cardiac fibroblasts, and establish a signaling circuit for epigenetic reprogramming in HF.

overall_design: RNA-Seq in ARVFs

first: Matthew

last: Stratton

first: Rushita

last: Bagchi

first: Rachel

last: Hirsch

first: Andrew

last: Riching

first: Marina

last: Felisbino

first: Blake

middle: Y

last: Enyart

first: Keith

last: Koch

first: Maria

last: Cavasin

first: Michael

last: Alexanian

first: Kunhua

last: Song

first: Jun

last: Qi

first: Madeleine

middle: E

last: Lemieux

first: Maggie

last: Lam

first: Saptarsi

last: Haldar

first: Charles

last: Lin


title: Dynamic chromatin targeting of BRD4 stimulates cardiac fibroblast activation

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: Dynamic chromatin targeting of BRD4 stimulates cardiac fibroblast activation [ChIP-seq]

overall_design: ChIP-Seq in ARVFs for Brd4 and RNA PolII

middle: A


title: Comparability of the small RNA secretome across human biofluids concomitantly collected from healthy adults

city: Cincinnati

first: Scott

last: Langevin

state: OH

address: 160 Panzeca Way, ML0056

department: Department of Environmental Health

institute: University of Cincinnati College of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Small extracellular vesicles (sEV) are nano-sized (40-150 nm), membrane-encapsulated vesicles that are released by malignant or pathologic and non-pathologic cells into the extracellular space and function as intercellular signaling vectors through the horizontal transfer of biologic molecules, including microRNA (miRNA) and other small non-coding RNA (ncRNA), that can alter the phenotype of recipient cells. sEV are present in essentially all extracellular biofluids, including serum, urine and saliva, and offer a new avenue for discovery and development of novel biomarkers of various disease states and exposures. The objective of this study was to determine the similarities and differences between sEV ncRNA derived from saliva, serum and urine, as well as cell-free ncRNA from serum. Saliva, urine and serum were concomitantly collected from 4 healthy donors, and sEV were isolated from each respective biofluid, along with cfRNA from serum. sEVs were isolated from the respective biofluids via differential ultracentrifugation. Small RNA-sequencing was performed on each sample, and cluster analysis was performed based on ncRNA profiles. While some similarities existed in terms of sEV ncRNA cargo across biofluids, there are also notable differences in ncRNA class and ncRNA secretion, with each sEVs in each biofluid bearing a unique ncRNA profile. We conclude that sEV ncRNA cargo varies according to biofluid, so thus should be carefully selected and interpreted when designing translational or epidemiological studies.

first: Mario

last: Medvedovic


title: Dynamic chromatin targeting of BRD4 stimulates cardiac fibroblast activation [RNA-seq_Mm]

first: Timothy

last: McKinsey

overall_design: RNA-Seq in mouse cardiac fibroblasts

first: Matthew

last: Stratton

middle: P


title: Transcriptional analysis of tenocytes from mice with a targeted deletion of scleraxis

status: Public on Feb 24 2020

city: New York

first: Christopher

middle: L

last: Mendias

state: NY

address: 535 E 70th St

institute: Hospital for Special Surgery

summary: We report RNA sequencing data from tenocytes cultured from the tail tendons of adult male mice in the C57Bl/6 background that either have the scleraxis gene (Scx+) or mice in which scleraxis has been deleted using CreERT2 driven from the Rosa26 locus using 4-hydroxytamoxifen (4HT).

overall_design: Differential expression of mRNAs were evaluated from tenocytes that contain (Scx+) or in which scleraxis was deleted (Scx-)


title: Transcriptional analysis of tendons and tenocytes from mice with a targeted deletion of scleraxis


title: Transcriptomic analysis of the soleus muscle extracted from Dnm2 K562E point-mutant heterozygous mice

city: Zurich

first: Jorge

middle: A.

last: Pereira

address: Otto-Stern-Weg 7

department: Dep. of Biology

institute: ETH Zurich

summary: RNA sequencing was performed to evaluate the impact of Dnm2 K562E mutation in the soleus muscle. The assessment of the dataset reveals a large number of differentially regulated transcripts between animals of both genotypes. This is consistent with a dominant phenotype caused by the Dnm2 K562E point mutation on the muscle.

overall_design: The dataset includes sequenced RNA extracted from soleus muscle of mice aged to 2 months. Soleus muscles were obtained from 4 independent male mice per genotype. The genotypes analyzed include controls (Dnm2+/+) and Dnm2 K562E point-mutant mice (Dnm2 +/K562E).

first: Joanne

last: Gerber

first: Daniel

first: Ueli

last: Suter


title: Combined mutation of C/EBPa and GATA-2 induce bi-lineage acute erythroid leukemia through transformation of a neomorphic neutrophil-erythroid progenitor [ATAC-seq]

city: Oxford

first: Cristina

last: Di Genua

address: Headley Way

department: Weatherall Institute of Molecular Medicine

institute: University of Oxford

summary: Acute erythroid leukemia (AEL) most commonly involves transformation of both the myeloid and erythroid lineages. However, the mutations that cause AEL and the nature of the transformed cell that sustains the bi-lineage leukemia phenotype remain unknown. We here show that combined bi-alleCD45.2+LKFcgRII/III+CD55- C/EBPa and GATA-2 zinc finger 1 (ZnF1) mutations are sufficient to induce bi-lineage AEL, and that the leukemia-initiating cell has a Lin–Sca-1–c-Kit+CD150–FcyRII/III+ surface phenotype, consistent with a committed myeloid progenitor. However, we find that in the presence of bi-alleCD45.2+LKFcgRII/III+CD55- C/EBPa mutation this cell population acquires ectopic erythroid gene expression and lineage potential, leading to the formation of neomorphic neutrophil-erythroid lineage progenitors, which upon transformation generate the bi-lineage leukemia-initiating cell. These results identify C/EBPa and GATA-2 ZnF1 mutations as causative of AEL, and demonstrate that transcriptional reprogramming by a leukemia-initiating mutation can re-define the lineage output of the resulting leukemia-initiating cells.

overall_design: ATAC-sequencing of bulk CD45.2+LKFcgRII/III+CD55- BM cells from 2-3 different competitively transplanted recipients at the pre-leukemic stage from CebpaK313KK/Lp30 (KL) and CebpaK313KK/Lp30;Gata2G320D/+ (KLG) mice as well as the corresponding leukemic stages from KL mice, KLG mice that develop a myeloid/erythroid leukemia (KLG-E), and KLG mice that develop a pure myeloid leukemia (KLG-M).

first: Claus

last: Nerlov


title: Examining the role of ATRX-RNA interactions in ATRX and PRC2 localization and gene expression.

city: Philadelphia

first: Kavitha

last: Sarma

address: 3601 Spruce St

institute: The Wistar Institute

summary: We disrupted the RNA binding region in endogenous ATRX and tested localization of ATRX, EZH2 and H3K27me3 by CUT&RUN.  We show that ATRX-RNA binding is important to regulate ATRX and PRC2 localization to specific genes.

overall_design: We performed CUT&RUN for ATRX, EZH2 and H3K27me3 in WT and ATRX△RBR (ATRX with RNA binding region deleted) using the protocol described in Skene et al, Nature protocols, 2018).  RNA Seq was performed in WT and ATRX△RBR.

first: Wenqing

last: Ren


title: Combined mutation of C/EBPa and GATA-2 induce bi-lineage acute erythroid leukemia through transformation of a neomorphic neutrophil-erythroid progenitor [RNA-seq]

overall_design: RNA-sequencing of bulk CD45.2+LKFcgRII/III+CD55-, CD45.1-EGFP-CD71hiTer119-/locKit+, and CD45.2+Mac1+cKitlo BM cells from three different competitively transplants recipients at pre-leukemic stage and corresponding leukemic populations in WT, Gata2G320D+ (G), CebpaK313KK/Lp30 (KL), and CebpaK313KK/Lp30;Gata2G320D/+ (KLG) mice


title: RNAseq of C57BL/6J and C57BL6/J Sarm1-deficient mice to determine if genes surrounding the knockout locus are B6 or 129 sequence

status: Public on Feb 23 2020

first: Melissa

last: Uccellini

address: 1468 Madison Ave

institute: Mt Sinai School of Medicine

summary: The Toll/IL-1R domain-containing adaptor protein SARM1 is expressed primarily in the brain, where it mediates axonal degeneration. Additional roles for SARM1 in a number of other processes including TLR-signaling, viral infection, chemokine expression, and XAF1 expression have also been described. Here we report defects in the induction of Ccl3, Ccl4, and Ccl5 in Sarm1-/- macrophages, for which we were unable to find mechanistic support. We instead show that the 129 congenic locus spans both the chemokine and XAF1 loci, and SNP analysis reveals other remaining 129 genomic regions in both existing knockout strains. New knockout mouse strains generated on a pure B6 genetic background using CRISPR confirmed the role of SARM1 in axonal degeneration and susceptibility WNV infection, but not in chemokine expression or susceptibility to VSV or LACV infection. We show that XAF1 expression differences are due to sequence and isoform polymorphism between B6 and 129 strains. Given its known role in apoptosis, XAF1 polymorphism may account for some phenotypes described in Sarm1-/- mice. RNAseq in the new CRISPR strains reveals changes in transcripts of the mitochondrial electron transport chain and ribosomal proteins, suggesting possible targets of SARM1.

overall_design: 1 sample from a WT mock infected mouse, 1 sample from a WT VSV infected mouse, 1 sample from a mock infected Sarm1-/- (Ding strain) mouse , 1 sample from a VSV infected Sarm1-/- (Ding strain) mouse


title: Combined mutation of C/EBPa and GATA-2 induce bi-lineage acute erythroid leukemia through transformation of a neomorphic neutrophil-erythroid progenitor [10x RNA-seq]

summary: Acute erythroid leukemia (AEL) most commonly involves transformation of both the myeloid and erythroid lineages.   However, the mutations that cause AEL and the nature of the transformed cell that sustains the bi-lineage leukemia phenotype remain unknown.   We here show that combined bi-alleCD45.2+LKFcgRII/III+CD55- C/EBPa and GATA-2 zinc finger 1 (ZnF1) mutations are sufficient to induce bi-lineage AEL, and that the leukemia-initiating cell has a Lin–Sca-1–c-Kit+CD150–FcyRII/III+ surface phenotype, consistent with a committed myeloid progenitor.   However, we find that in the presence of bi-alleCD45.2+LKFcgRII/III+CD55- C/EBPa mutation this cell population acquires ectopic erythroid gene expression and lineage potential, leading to the formation of neomorphic neutrophil-erythroid lineage progenitors, which upon transformation generate the bi-lineage leukemia-initiating cell.   These results identify C/EBPa and GATA-2 ZnF1 mutations as causative of AEL, and demonstrate that transcriptional reprogramming by a leukemia-initiating mutation can re-define the lineage output of the resulting leukemia-initiating cells

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: The design for the 10x sort was: 8700 Lin-CD71+CD235a+ and 8700 Lin-CD71-CD235a- single cells were sorted from two human AEL samples and 15000 Lin-CD45. 1-GFP- single cells were sorted from two KLG-E mice. Libraries were preparing using the chromium single cell 3’ reagent kits v2 (10x Genomics, California USA) according to manufacturer’s protocol.

first: Supat

last: Thongjuea


title: Combined mutation of C/EBPa and GATA-2 induce bi-lineage acute erythroid leukemia through transformation of a neomorphic neutrophil-erythroid progenitor

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


title: Differential gene expression in the brainstem of uninfected and West Nile Virus infected C57BL6/J and Sarm1-em3AGS mice

overall_design: 12 samples were analyzed, each in triplicate biological samples. Mock samples are individual mice, infected samples are pools of 2-3 mice


title: Gene expression profile of D2.OR-EGFP and D2.A1-EGFP cells in vitro and in vivo

city: Padova

first: Marco

last: Montagner

state: PD

address: viale G. Colombo, 3

country: Italy

institute: University of Padua

summary: We analysed gene expression profiles of D2.OR-EGFP and D2.A1-EGFP cells isolated from lungs and under standard in vitro conditions

overall_design: BALB/c nude female mice (6- to 8-weeks old) were injected in tail vein with 1x106 D2.A1-eGFP cells or D2.OR-eGFP cells. After 3 weeks, lungs were collected, digested to single cell suspension and stained with CD45-APC antibody. CD45-/eGFP+ cells were FACS sorted and RNA purified. For in vitro samples, breast cancer cells were grown in multiwell plates under standard culture conditions, trypsinised, sorted and processed in parallel with the in vivo samples.

first: Erik

last: Sahai

first: Steven

last: Hooper

first: Probir

last: Chakravarty


title: RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells

city: La Jolla

middle: Jen-Yue

last: Wei

state: CA

address: 9500 Gilman Dr

department: Bioengineering

institute: University of California, San Diego

type: Methylation profiling by high throughput sequencing

summary: Retrospective lineage tracing harnesses naturally occurring mutations in cells to elucidate single cell development.  Common single cell phylogenetic fate mapping methods have utilized highly mutable microsatellite loci found within the human genome.  Such methods were limited by the introduction of in vitro noise through polymerase slippage inherent in DNA amplification, which we characterized to be approximately 10-100 higher than in vivo replication mutation rate.  Here, we present RETrace, a method for simultaneously capturing both microsatellites and methylation-informative cytosines to characterize both lineage and cell type, respectively, from the same single cell.  An important unique feature of RETrace was the introduction of linear amplification of microsatellites in order to reduce in vitro amplification noise.  We further coupled microsatellite capture with single-cell reduced representation bisulfite sequencing (scRRBS), to measure the CpG methylation status on the same cell for cell type inference.  When compared to existing retrospective lineage tracing methods, RETrace achieved higher accuracy (88% triplet accuracy from an ex vivo HCT116 tree) at a higher cell division resolution (lowering the required number of cell division difference between single cells by approximately 100 divisions).  Simultaneously, RETrace demonstrated the ability to capture on average 150,000 unique CpGs per single cell in order to accurately determine cell type.  We further formulated additional developments that would allow high-resolution mapping on microsatellite stable cells or tissues with RETrace. Overall, we present RETrace as a foundation for multi-omics lineage mapping and cell typing of single cells.

overall_design: 138 HCT116, 67 U87MG, and 137 adult post-mortem single cells/nuclei  were processed along with respective bulk

middle: J

first: Kun

last: Zhang


title: Effect of acute inhibition of cMET signaling in MET amplified MTB-TAN recurrent xenograft tumor in vivo.

first: Lewis

last: Chodosh

state: Pennsylvania

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

summary: cMET is a well known oncogene whose activation is widely implicated in tumorigenesis and metastasis.  To investigate the effects of acute inhibitoin of cMET signaling in the mammary tumors, we inhibited cMET activation in xenograft mammary tumors that were derived from a MET amplified mouse mammary tumor cell line and analyzed the transcriptional alteration between vehicle and MET inhibitor treated tumors.

overall_design: 12 hour treatment of MET inhibitor or vehicle in mice with xenograft tumors,  six replicates per treatment.

first: Dhruv

middle: K

last: Pant

first: Yi

last: Feng


title: Hypoxia and HIF-1α Regulate Collagen Production in Keloids

status: Public on Feb 22 2020

city: boston

first: Hensin

last: Tsao

state: Massachusetts

address: 50 Blossom Street

institute: massachusette general hospital

summary: Keloids are reactive or spontaneous fibroproliferative dermal tumors characterized by the exaggerated and uncontrolled accumulation of extracellular collagen. Current approaches to mitigate keloidogenesis are largely procedural in nature.  However, a better understanding of its biological drivers may lead to novel targeted treatments for keloids. Through whole-genome expression analysis, we found that a HIF-1α transcriptional footprint is preferentially upregulated (activation score=2.024; p=1.05E-19) in keloid fibroblasts (KFs) compared to normal dermal fibroblasts (NFs).  We verified that HIF-1α protein is more strongly expressed in keloid specimens compared to normal skin (p=0.035) and that hypoxia (1% O2) leads to increased collagen, especially in the extracellular compartment. Collagen levels were uniformly reduced by selective HIF-1α inhibitor CAY10585.  Our results indicate that collagen secretion may be intimately linked to a hypoxic microenvironment within keloid tumors and that HIF-1α blockade could be a novel avenue of treatment for these tumors.

overall_design: Briefly, 10 cell lines (5 NFs and 5 KFs) were grown in replicate cultures and subjected to RNA extraction using the Qiagen RNeasy Mini Kit (Qiagen). 100 ng of total mRNA from 20 samples (10 cell lines in duplicate) were then sent to the Whitehead Institute Genome Technology (WIGT) Core for expression profiling.    Standard operating procedures at the WIGT Core are summarized.  RNA quality was analyzed using an Agilent 2100 Bioanalyzer. After QC, one of the keloid samples was removed leaving a total of 19 samples (10 NFs and 9 KFs).  Briefly, RNA samples with RNA integrity number (RIN) above 9.8 were hybridized to GeneChip PrimeView Human Gene Expression Arrays (Affymetrix,) and analyzed using GeneChip Expression Console. A Primeview CDF (provided by Affymetrix) that included probe information for the ERCC controls (GPL16043) was used to generate the CEL files.

first: Yuanyuan

last: Kang

first: Mi

last: Roh

first: Suvi

last: Rajadurai


title: Effect of acute HGF-induced cMET activation  in MCF10A cells in vitro

summary: cMET is a well known oncogene whose activation is widely implicated in tumorigenesis and metastasis.  To investigate the effects of acute activation of cMET signaling in the mammary epithelial cells, we stimulated MCF10A cells with increasing doses of HGF and analyzed the transcriptional alteration between PBS and HGF treated cells.

overall_design: MCF10A cells were treated with 0ng, 1ng, 3ng, 7.5ng, 15ng  and  30ng HGF with four replicates per dosage for 4hrs


title: cMET

overall_design: Refer to individual Series


title: Effects of PXR activation on the macrophage transcriptome

city: RIVERSIDE

first: ZHAOJIE

last: MENG

address: 900 UNIVERSITY AVENUE

institute: UNIVERSITY OF CALIFORNIA, RIVERSIDE

summary:
Purpose: To explore the role of PXR signaling in regulating macrophage transcriptome related to atherogenesis
Methods: Peritoneal macrophages were isolated from LDLR knockout mice with myeloid specific PXR deficiency (PXRΔMyeLDLR-/-) and their littermates (PXRF/FLDLR-/-). Then the macrophages were treated with a PXR ligand PCN  or DMSO control for 12 hr. Total RNA was extracted for RNAseq
Results: PCN-mediated PXR activation induced 439 differentially expressed genes (DEGs) with false discovery rate (FDR) < 5% and fold change >1.5 in control macrophages.  By contrast, PCN only induced 38 DEFs in PXR-deficient macrophages.
Conclusions: These results indicate that PXR signaling may affect many genes in macrophages related atherosclerosis development.

overall_design: Macrophagic mRNA profiles of control and PXR-deficient  macrophages after 12-hr treatment of PXR ligand PCN

first: Zhaojie

last: Meng

first: Tong

last: Zhou

first: Changcheng


title: Mitochondrial dysfunction and DNA damage accompany enhanced levels of formaldehyde in cultured primary human fibroblasts

city: Research Triangle Park

first: Cristina

last: Nadalutti

state: NC

address: 111 T W Alexander Dr., A030 Rall Bldg.

department: Genome Integrity and Structural Biology Laboratory

institute: National Institute of Environmental Health Sciences

summary:
Formaldehyde (FA) is a simple biological aldehyde that is produced inside cells and its accumulation is known to be cytotoxic. We choose to use primary human fibroblasts cells in culture (foreskin, FSK) as a physiological model to gain insight into whether an increase in the level of FA might affect cellular physiology, especially with regard to the mitochondrial compartment.
Gene expression assessment by microarray analysis revealed FA affected FSK cells by altering expression of many genes including genes involved in mitochondrial function and electron transport. We were surprised to observe increased DNA double-strand breaks (DSBs) in mitochondria after exposure to FA, as revealed by accumulation of γH2A.X and 53BP1 at mitochondrial DNA foci. This was associated with mitochondrial structural rearrangements, loss of mitochondrial membrane potential and activation of mitophagy. Collectively, these results indicate that an increase in the cellular level of FA can trigger mitochondrial DNA double-strand breaks and dysfunction.

overall_design: Gene expression in FSK cells was measured at 24 hours after exposure to 250 μM FA .  Three independent experiments were performed.

first: Samuel

middle: H

last: Wilson

first: Kevin

last: Gerrish

first: Ashley

last: Brooks


title: Expression Profiling of U2OS Cell Lines Transfected with MicroRNA-571 Mimic or MicroRNA-571 Inhibitor vs. MicroRNA-Control Transfected U2OS Cell Lines

city: WASHINGTON

first: Wenge

last: Zhu

state: DC

address: 800 22ND ST NW, Room 8480, Science & Engineering Hall

department: Biochemistry and Molecular Medicine

institute: George Washington University

summary: Osteosarcoma U2OS cells were studied to profile the expression of miR-571 mimic & inhibitor transfected cells. The goal was to gain insights or to build hypotheses into the mechanisms of miR-571 regulation effects on the DNA replication network in cell-based model.

overall_design: The study included three experimental groups, U2OS miR-571 mimic transfected  cells, U2OS miR-571 inhibitor transfected cells and U2OS miR control transfected cells.  Each group had two biological replciate samples.

first: Jing

last: Sun

first: Zhuqing

last: Li


title: The role of lncRNA Sarrah in human cardiomyocytes

city: Amsterdam

first: Reinier

last: Boon

address: De Boelelaan 1117

country: Netherlands

institute: Amsterdam UMC

summary: Long non-coding RNAs (lncRNAs) contribute to (patho)physiological processes in the heart. Aging is the major risk factor for cardiovascular disease and cardiomyocyte apoptosis is an underlying cause for age-related cardiac dysfunction. RNA sequencing of cardiomyocytes from young and aged mouse hearts revealed several aging-regulated lncRNAs. An siRNA screen for caspase activity identified the aging-regulated lncRNA Sarrah (ENSMUST00000140003) as anti-apoptotic, which we confirmed in human cells (human SARRAH is annotated as OXCT1-AS1). Importantly, human engineered heart tissue showed impaired contractile force development upon SARRAH knockdown compared with controls. Computational prediction of RNA-DNA triple helix formation showed that SARRAH may directly bind the promoters of genes downregulated after SARRAH silencing, which mainly consist of cell survival genes. Indeed, nuclear magnetic resonance spectroscopy confirmed RNA-DNA triple helix formation and cardiomyocytes lacking the triple helix-forming domain of Sarrah showed an increase in apoptosis. One of the key direct SARRAH targets is NRF2, an anti-oxidant transcription factor. Restoration of NRF2 levels after SARRAH silencing partially rescues the reduction in cell viability. RNA affinity purification mass spectrometry analysis identified CRIP2 as main protein interaction partner. Furthermore, SARRAH associates with acetyltransferase p300 and acetylated histone H3K27. Finally, Sarrah was also profoundly downregulated after acute myocardial infarction (AMI) in mice. Adeno-associated virus-mediated overexpression of Sarrah in mice showed better recovery of cardiac contractile function after AMI compared to control mice, as measured by echocardiography and magnetic resonance imaging, consistent with a decrease in cardiomyocyte cell death and an increase in endothelial cell proliferation. In summary, we identified the anti-apoptotic evolutionary conserved lncRNA Sarrah, which is downregulated by aging, as a pivotal regulator of cardiomyocyte survival. Sarrah overexpression has beneficial effects on AMI recovery highlighting it as a potential therapeutic approach against heart failure.

overall_design: 3 replicates human cardiomyocytes were transfected with control gapmeRs and, in parallel, 3 replicates human cardiomyocytes were transfected with gapmeRs targeting lncRNA Sarrah

first: D

last: Trembinski


title: Pathogen-pathogen interactions, a way to soothe virulence?

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

institute: university of Groningen

summary: In planktonic and biofilm mimicking environments, the staphyloccocal transcriptome in t111+t13595 co-cultures  showed significant upregulation of genes related to virulence factors contrary to those co-cultures with B. thuringiesis and K. oxytoca.  In the biofilm polymicrobial environment, S. aureus transcriptome shows extensive downregulation of gene expression. The animal model co-infection with S. aureus and K. oxytoca proved to be less virulent than when infected only with S. aureus alone, or K. oxytoca alone where higher infection and mortality rates were observed.

sample_organism:
Klebsiella oxytoca
Staphylococcus aureus
Bacillus thuringiensis

overall_design: Two Staphylococcus aureus strains, one Bacillus thuringiensis, and one Klebsiella oxytoca strains. Twenty three different conditions.

first: Andrea

middle: N

last: García-Pérez

first: Jan

middle: M

last: van Dijl

last: de Jong


title: Deconvolution of myeloid cell cytokine specific transcriptional profiles during tuberculosis and cancer identifies neutrophil activation as a prognostic feature

status: Public on Feb 21 2020

first: Joseph

middle: C

last: Devlin

address: 430 East 29th Street

department: Microbiology

institute: New York University Langone Health


title: N3-Kethoxal-seq for genome-wide RNA structure mapping in vivo

city: Wuhan

first: Xiaocheng

last: Weng

address: Bayi Road

department: School of Pharmaceutical Sciences

institute: Wuhan University

summary: We established N3-Kethoxal molecule to probe RNA secondary structure in vivo at transcriptome level.

overall_design: Libraries treated with N3-kethoxal, kethoxal-remove and no treat were prepared, and the RNAs are extracted and for sequencing.

last: Gong

first: Yi

last: Chen

first: Qiangfeng

last: Zhang

first: Xiang

first: Chuan

last: He


title: RNA-seq of rd1 retinal microglia after treatment with AAV8-GFP vs. AAV8-GFP + AAV8-TGFB1

city: Stanford

first: Sean

last: Wang

address: 269 Campus Drive

department: Genetics

institute: Stanford University

summary: Transcriptional profiling of microglia (seven biological replicates per experimental condition) or non-microglia (four biological replicates total). One thousand microglia (CD11b+ Ly6G/Ly6C-) or non-microglia cells (CD11b-) from P30 rd1 (FVB) retinas infected with either AAV8-GFP or AAV8-GFP + AAV8-TGFB1 were sorted into 10 µL of Buffer TCL (Qiagen) containing 1% beta-mercaptoethanol and immediately frozen on dry ice. Samples were subsequently sent to the Broad Institute Genomics Platform for cDNA library synthesis and sequencing using a modified Smart-Seq2 protocol with an expected coverage of ~6 million reads per sample. Prior to analysis, reads were subjected to quality control measures and mapped to the GRCm38.p6 reference genome. Reads assigned to each gene were then quantified using featureCounts and normalized and analyzed for differential expression using DESeq2.

overall_design: RNA-seq of microglia and non-microglia from P30 rd1 (FVB) retinas treated with AAV8-GFP vs. AAV8-GFP + AAV8-TGFB1

first: Constance

last: Cepko


title: Deconvolution of myeloid cell cytokine specific transcriptional profiles during tuberculosis and cancer identifies neutrophil activation as a prognostic feature [whole blood]

summary: The cytokine environment and cellular infiltrate during an inflammatory response may contain prognostic features that could guide therapy or predict disease outcome. Here we analyzed the transcriptional responses of human monocytes, macrophages, dendritic cells and neutrophils to stimulation by type 1 cytokines (IFN-g, IFN-b and IFN-l) type 2 cytokines (IL-4 and IL-13) and the immunoregulatory cytokine IL-10. This generated a myeloid cell cytokine specific response matrix to infer representation of myeloid cells and the cytokine environment they may encounter during infection and in tumors. Neutrophils were surprisingly responsive to type 1 and type 2 cytokine stimulation but did not respond to IL-10. We identified transcripts specific to IFN-b stimulation, whereas other IFN signature genes were upregulated by both IFN-g and IFN-b. When used to deconvolute blood profiles from tuberculosis patients, the IFN-b specific neutrophil signature was surprisingly reduced in TB patients with active disease whereas the shared response to IFN-g and IFN-b in neutrophils was increased. When applied to glioma patients, transcripts of neutrophils exposed to IL-4 or IL-13 and monocyte responses to IFN-g or IFN-b emerged as opposing predictors of survival in samples from patients with glioma. This approach may help delineate biological roles for myeloid cells in different cytokine environments during disease processes.

overall_design: Stimulation of whole blood from 3 anonymous healthy human donors with 6 cytokines

first: Erin

last: Zwack

first: P'ng

last: Loke

first: Victor

last: Torres


title: Expression data from human non-affected and cancerous colon

city: Stockholm

first: Anna

last: Rao

address: Alfred Nobels Alle 8

department: Center for Infectious Medicine (CIM)

country: Sweden

institute: Karolinska Institutet

summary: Innate lymphoid cells (ILCs) have the ability to sense and amplify inflammatory signals, and have been shown to exert bi-directional regulation with T helper cells in mice. However, how crosstalk between ILCs and CD4+ T cells influences immune function in humans is unknown. We observed that human intestinal ILCs co-localize with T cells in healthy and colorectal cancer tissue and display elevated HLA-DR expression in tumor and tumor-adjacent areas. Although mostly lacking co-stimulatory molecules ex vivo, intestinal and peripheral blood ILCs acquired antigen-presenting characteristics triggered by inflammasome-associated cytokines IL-1β and IL-18. This effect was strongly inhibited by the anti-inflammatory cytokine TGFβ. Here we wanted to investigate how the microenvironment in the colon would change in the cancer setting. We used microarrays to profile global gene expression changes in the human colon, extending from non-affected tissue with increasing proximity to cancerous tissue.

overall_design: Non-affected, tumor border and central tumor tissue was obtained from 3 patients undergoing colon cancer surgery. Muscle and adipose tissues were removed and a small piece (approximately 2x2mm) of the remaining non-affected as well as cancer-associated colon tissue was used for RNA extraction and hybridization on Affymetrix microarrays.

first: Jenny

last: Mjösberg


title: scRNA-seq analyses on Thy1.1+Thy1.2+ MDR1-sufficient and Thy1.1+Thy1.2- MDR1-deficient P14 CD8+ T cells from ten congenically-transferred and LCMV-infected wild type B6 mice at day 8 post-infection

city: Jupiter

first: Mark

last: Sundrud

state: FL

address: 120 Scripps Way

department: Immunology and Microbiology

institute: The Scripps Research Institute

summary: Multidrug resistance (MDR)-1 acts as a chemotherapeutic drug efflux pump in tumor cells, although its physiologic functions remain enigmatic. Using a recently-developed MDR1-knockin reporter allele (Abcb1aAME/+), we found that constitutive MDR1 expression amongst hematopoietic cells was observed mainly in cytolytic lymphocytes—including CD8+ cytotoxic T lymphocytes (CTL) and natural killer cells—and regulated by Runt-related (Runx) transcription factors. Although MDR1 was dispensable for naïve CD8+ T cell development, it was required for both normal accumulation of effector CTL following acute viral infection and protective function of memory CTL upon challenge with an intracellular bacterium. MDR1 acted early after naïve CD8+ T cell activation to suppress oxidative stress, enforce survival and safeguard mitochondrial function in developing CTL. Together, these data highlight an important endogenous function of MDR1 in cell-mediated immune responses, and suggest that ongoing efforts to intentionally inhibit MDR1 in cancer patients could be counter-productive.

overall_design: scRNA-seq analyses was performed on FACS-purified Thy1.1+Thy1.2+ MDR1-sufficient and Thy1.1+Thy1.2- MDR1-deficient P14 CD8+ T cells from ten congenically-transferred and LCMV-infected wild type B6 mice at day 8 post-infection

first: M

first: A

last: Getzler


title: Induction of steatohepatitis and liver tumorigenesis by enforced Snail expression in hepatocytes

city: Fukuoka

first: Atsushi

last: Suzuki

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

department: Division of Organogenesis and Regeneration

institute: Medical Institute of Bioreguration, Kyushu University

summary: Enforced Snail expression in hepatocytes is sufficient for induction of steatohepatitis and liver tumorigenesis through disruption of the biliary canaliculus and bile acid homeostasis in the liver.

overall_design: We conducted comparative global gene expression analyses between the liver of wild-type (WT) mouse and that of Alb-Cre;CAG-floxed neo-Snail mouse.

first: S

last: Miura


title: Rice gene expression analysis

city: Kunming

first: Gang

last: Liang

address: Xuefu Road 88, Wuhua district

institute: Xishuangbanna Tropical Botanical Garden,CAS

summary: Four-day-old seedlings germinated in wet paper were transferred to solution culture with 0.1 mM Fe(III)-EDTA for five days. Then seedlings were transferred to solution culture without Fe or with 0.1 mM Fe(III)-EDTA for five days. Roots and shoots were separated and used for RNA extraction.

overall_design: Roots and shoots were separately harvested. For each sample, three biological replicates were pooled and mixed as one sample.

first: Diqu

last: Yu


title: Pooled CRISPR screens in human intestinal organoids [CRISPR screens]

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

institute: ETH/University of Zurich

summary: We performed CRISPR screens on both a sub-library and a genome-wide scale in human intestinal organoids to discover cancer driver genes. We investigated the Wnt and the TGFB pathway and used both WT, APC-mutant and APC-TP53-mutant organoids.

overall_design: We used lentiviral transduction of CRISPR-Cas9-sgRNA libraries in human intestinal organoids. After selection, we amplified sgRNA sequences and performed amplicon sequencing.

first: Till

last: Ringel

first: Nina

last: Frey

first: Femke

last: Ringnalda

first: Sharan

last: Janjuah

first: Sarah

last: Cherkaoui

first: Stefan

last: Butz

first: Sumana

last: Srivatsa

first: Martin

last: Pirkl

first: Giancarlo

last: Russo

first: Lukas

last: Villiger

first: Gerhard

last: Rogler

first: Hans

last: Clevers

first: Niko

last: Beerenwinkel

first: Nicola

last: Zamboni

first: Tuncay

last: Baubec

first: Gerald

last: Schwank


title: ChromID identifies the protein interactome at chromatin marks

city: Utrecht

address: Padualaan 8

department: Department of Biology

institute: Utrecht University

summary: Chromatin modifications regulate genome function by recruiting protein factors to the genome. However, the protein composition at distinct chromatin modifications has yet to be fully characterized. In this study, we used natural protein domains as modular building blocks to develop engineered chromatin readers (eCRs) selective for DNA methylation and histone trimethylation at H3K4, H3K9 and H3K27 residues. We first demonstrated their utility as selective chromatin binders in living cells by stably expressing eCRs in mouse embryonic stem cells and measuring their subnuclear localization, genomic distribution and histone-modification-binding preference. By fusing eCRs to the biotin ligase BASU, we established ChromID, a method for identifying the chromatin-dependent protein interactome on the basis of proximity biotinylation, and applied it to distinct chromatin modifications in mouse stem cells. Using a synthetic dual-modification reader, we also uncovered the protein composition at bivalently modified promoters marked by H3K4me3 and H3K27me3. These results highlight the ability of ChromID to obtain a detailed view of protein interaction networks on chromatin.

overall_design: Chromatin immunoprecipitation from crosslinked mouse embryonic stem cells expressing biotin-tagged synthetic proteins.

first: Rodrigo

last: Villasenor


title: Identification of enhancer landscape in MDA-MB-231 cells

city: Cleveland

first: Ruth

last: Keri

address: 9500 Euclid Avenue

institute: Cleveland Clinic Lerner Research Institute

summary: To identify typical enhancers and super-enhancers in the MDA-MB-231 triple-negative breast cancer cell line, we performed ChIP-seq using DNA isolated from untreated MDA-MB-231 cells using an H3K27ac antibody.

overall_design: Examination of H3K27ac binding profiles in MDA-MB-231 cells

first: Jennifer

last: Sahni

first: Bryan

last: Webb


title: Cellular microRNAs in Huh7.5.1 cells

status: Public on Feb 20 2020

city: Strasbourg

first: Sébastien

last: Pfeffer

address: 2 allée Konrad Roentgen

department: UPR 9002 - Architecture et Réactivité de l'ARN

country: France

institute: CNRS - Institut de Biologie Moléculaire et Cellulaire (IBMC)

summary: Small RNAs play a critical role in host-pathogen interaction and microRNAs have emerged as key regulators of viral infections. Based on this evidence, we wished to contribute to this research field by identifying and characterizing cellular microRNAs with a positive or negative role on Sindbis virus (SINV) infection.

overall_design: Taking advantage of large scale sequencing, we cloned and sequenced small RNAs from Huh7.5.1 cells. We analyzed the expression levels of cellular microRNAs and we compared with the results of a mimic genome-wide screening using SINV-GFP as reporter. Altogether, our results indicate a positive role for the cellular miR-124-3p in SINV infection.

first: Paula

last: López

first: Erika

last: Girardi

last: Mounce

first: Amélie

last: Weiss

first: Béatrice

last: Chane-Woon-Ming

first: Mélanie

last: Messmer

first: Pasi

last: Kaukinen

first: Arnaud

last: Kopp

first: Diane

last: Bortolamiol-Becet

first: Ali

last: Fendri

first: Marco

last: Vignuzzi

first: Laurent

last: Brino


title: GPR160 de-orphanization reveals critical roles in neuropathic pain in rodents

city: St. Louis

first: Jinsong

last: Zhang

state: MO

address: 1402 South Grand Blvd.

department: Department of Pharmacology & Physiology

institute: Saint Louis University School of Medicine

summary: Treating neuropathic pain is challenging and novel non-opioid based medicines are needed. Using unbiased receptomics, transcriptomic analyses, immunofluorescence and in situ hybridization, expression of the orphan GPCR (oGPCR) GPR160 increased in the rodent dorsal horn of the spinal cord (DH-SC) following traumatic nerve injury. Genetic and immunopharmacological approaches demonstrated that GPR160 inhibition in the spinal cord prevented and reversed neuropathic pain in male and female rodents without altering normal pain response. GPR160 inhibition in the spinal cord attenuated sensory processing in the thalamus, a key relay in the sensory discriminative pathways of pain. We also identified cocaine- and amphetamine-regulated transcript peptide (CARTp) as a GPR160 ligand. Inhibiting endogenous CARTp signaling in spinal cord attenuated neuropathic pain, whereas exogenous intrathecal (i.th.) CARTp evoked painful hypersensitivity through GPR160-dependent ERK and cAMP response element-binding protein (CREB). Our findings de-orphanize GPR160, identify it as a determinant of neuropathic pain and potential therapeutic target, and provide insights to its signaling pathways. CARTp is involved in many diseases including depression, reward and addiction, de-orphanization of GPR160 is a major step forward understanding the role of CARTp signaling in health and disease.

overall_design: Methods: The dorsal horn of the spinal cord (lumbar L4-L6) was harvested on d9 post CCI or SHAM surgery. Tissues were immediately preserved in RNALater® overnight at 4°C. Total RNA was isolated the next day using RNeasy® Plus Universal Mini Kit (Qiagen, Germantown, MD USA) and quantitated by NanoDropTM (ThermoFisher Scientific). Total RNA samples were assessed for RNA quality and sequenced by the Genome Technology Access Center (GTAC) at Washington University in Saint Louis using Illumina HiSeq. Gene expression was normalized using Kallisto followed by Trimmed Mean of M-values methods and differential gene expression between CCI and SHAM groups were tested using negative binomial and generalized linear regression models by edgeR. Differentially expressed genes were defined as those with a fold change >=1.5-fold and a false discovery rate (FDR) <=0.05.

first: Timothy

last: Doyle

first: Daniela

last: Salvemini


title: BAF60a deficiency uncouples chromatin accessibility and cold sensitivity from white fat browning

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Ave

department: Cell & Developmental Biology, Life Science Institute

institute: University of Michigan

summary: Brown and beige fat share a remarkably similar transcriptional program that supports fuel oxidation and thermogenesis. The chromatin-remodeling machinery that governs genome accessibility and renders adipocytes poised for thermogenic activation remains elusive. Here we found that BAF60a, a subunit of the SWI/SNF chromatin-remodeling complexes, serves an indispensible role in cold-induced thermogenesis in brown fat. BAF60a maintains chromatin accessibility for key thermogenic genes in close proximity to PPARg and EBF2 binding sites. Surprisingly, fat-specific BAF60a inactivation triggers more pronounced browning of inguinal white adipose tissue that is linked to induction of MC2R, a receptor for the pituitary hormone ACTH. Elevated MC2R expression sensitizes adipocytes and BAF60a-deficient adipose tissue to thermogenic activation in response to ACTH stimulation. These observations reveal an unexpected dichotomous role of BAF60a-mediated chromatin remodeling in transcriptional control of brown and beige gene programs and illustrate a pituitary-adipose signaling axis in the control of thermogenesis.

overall_design: ATAC-seq on control and Baf60a KO mouse brown adipose tissue, each sample contains two technical replicates which have been performed Tn5 transposase reaction independently.

first: Tongyu

last: Liu

first: Lin

last: Mi

first: Siming

last: Li


title: The embryonic linker histone dBigH1 compromises the functional epigenetic state of active chromatin

city: Barcelona

first: Oscar

last: Reina Garcia

state: Barcelona

address: C/Baldiri Reixac 10

department: Biostatistics and Bioinformatics

institute: IRB Barcelona

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

overall_design: Refer to individual Series


title: Regional gene expression profiling upon loss of NFIA in adult astrocytes

city: Houston

first: Brittney

last: Lozzi

state: TX

address: 1 Baylor Plaza

department: Cell & Gene Therapy

institute: Baylor College of Medicine

summary: The goal of this study is to determine how the loss of the transcription factor NFIA affects the molecular profiles of adult astrocytes from four brain regions. We performed RNA-sequencing on control and NFIA knockout (KO) astrocytes from the olfactory bulb, hippocampus, cortex, and brainstem, and analyzed the molecular signatures of NFIA KO astrocytes compared to control in each brain region.

overall_design: Using our NFIAfl/fl; Aldh1l1-CreER; Aldh1l1-GFP (AAG) mouse line we conditionally knocked out NFIA only in astrocytes. FAC sorted astrocytes from the olfactory bulb, hippocampus, cortex, and brainstem of 5-month-old mice were collected in triplicate from our AAG mouse line and NFIAfl/fl; Aldh1l1-GFP mice for controls. AAG and control astrocytes were molecularly profiled using RNA-sequencing.

first: Anna

last: Huang

first: Benjamin

last: Deneen


title: Transcriptome Analysis of Wild Type and OsMYB305 Overexpressed Rice

city: wuhan

first: wang

last: dujun

state: hubei

address: No.1,Shizishan Street · Hongshan District

institute: Huazhong Agricultural University

summary: The goals of this study are to identify the differentially expressed genes in the roots of OsMYB305 overexpressed Rice growing under low nitrogen condition.

overall_design: Root mRNA profiles of wild-type (WT) and  OsMYB305 overexpressed Rice growing under low nitrogen condition for 14 days were generated by deep sequencing, in bipartite, using HiseqXten-PE150. The sequence reads were first filtered  with the FastQC v0.11.8;then pre-processed using the Trimmomatic-0.38;then mapping with Hisat2 v2.1.0;finally differentially-expressed genes(DEGs) were identified using the Cufflinks v2.2.  OE15 and OE20 are independent transgenic lines of OsMYB305  which have very similar phenotypes compared to WT under low N treatment: growth advantages, increased N concentrations, decreased cellulose contents, etc.

first: Dujun

last: Wang

first: Zikui

last: Yin


title: Expression analysis of MADM based glioma mouse model and normal brain

city: Nagoya

first: Keisuke

last: Katsushima

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku

department: Department of Epigenomics

institute: Nagoya City University Graduate School of Medical Sciences

summary: Mosaic Analysis with Double Markers (MADM) based glioma mouse model, which homozygously lacks Tp53 and Nf1, spontaneously developed gliomas at the post-natal 90-120 days. Tp53 and Nf1 are among the most frequently mutated genes in human glioma patients. Investigating the expression changes of genes induced by inactivation of Tp53, Nf1 and EZH2 can be a clue to clarify the mechanism of gliomagenesis. We examined the expressions of glioma cells in MADM mouse (n=2), EZH2 knocked-out MADM glioma tissues (n=3) and neural stem cell (NSC), astrocyte established with normal mice brains (n=2, respectively) and TP53 knocked-out astrocytes, derived from TP53 knocked-out mice (n=2). We used SurePrint G3 Mouse GE 8×60K array slides (G4858A, Agilent Technologies).

overall_design: Microarray experiment was performed as single-color hybridization on SurePrint G3 Mouse GE 8 x 60K array.

first: Fumiharu

last: Ohka

first: Shoichi

last: Deguchi

first: Keiko

last: Shinjo

first: Toshihiko

last: Wakabayashi

first: Atsushi

last: Natsume

first: Yutaka

last: Kondo


title: Continuous mitotic activity of primitive hematopoietic stem cells in adult mice

city: Dresden

first: Alexander

last: Gerbaulet

state: Saxony

address: Fetscherstr. 74

department: Institute for Immunology

institute: Medical Faculty TU Dresden

summary: Transcriptomes of 282 single HSC (LSK CD48-lo/CD150+) isolated from bone marrow of un-induced Col1a1 H2B-GFP xR26rtTA mice

overall_design: single HSCs (LSK CD48-/loCD150+) were isolated from un-induced R26rtTA/rtTA/Col1A1H2B-GFP/H2B-GFP mice (n= 6, aged 12 – 22 wks, two independent experiments).


title: RNA sequencing of COH29 treatment in C4-2 cells

city: New York

first: Bic

last: MSKCC

address: 1275 York Ave.

institute: Memorial SLoan-Kettering Cancer Center

summary: Human prostate cancer C4-2 cells treated with COH29 and DMSO. Cells were treated with DMSO, 10uM or 20 uM COH29 for 48 hours. Cells were prepared for RNA-seq.

overall_design: To understand the mechanisms of RRM2 inhibition by COH29 in Human prostan cencer cells. RNA sequencing were were analysed by Partek  flow

first: Ying

middle: Z

last: Mazzu

first: Philip

last: Kantoff


title: ChIP and expression analysis of MADM based glioma mouse model

type: Genome binding/occupancy profiling by genome tiling array


title: Transcriptional diversity and bioenergetic shift in human breast cancer metastasis revealed by single-cell RNA sequencing

city: Irvine

first: Devon

last: Lawson

address: 839 Health Science Road, Sprague Hall 114

department: Physiology and Biophysics

institute: UC Irvine

summary: Although metastasis remains the cause of most cancer-related mortality, mechanisms governing seeding in distal tissues are poorly understood. Here we establish a robust method for identification of global transcriptomic changes in rare metastatic cells during seeding using single-cell RNA-sequencing and patient-derived xenograft (PDX) models of breast cancer. We find that both primary tumours and micrometastases display transcriptional heterogeneity, but micrometastases harbor a distinct transcriptome program conserved across PDX models that is highly predictive of poor survival in patients. Pathway analysis revealed mitochondrial oxidative phosphorylation (OXPHOS) as the top pathway upregulated in micrometastases, in contrast to higher levels of glycolytic enzymes in primary tumour cells, which we corroborated by flow cytometric and metabolomic analyses. Pharmacological inhibition of OXPHOS dramatically attenuated metastatic seeding in the lungs, which demonstrates the functional importance of OXPHOS in seeding and highlights its potential as a therapeutic target to prevent metastatic spread in breast cancer patients.

overall_design: Analysis of single cell transcriptome changes between primary tumors and metastasis in mice PDX models of breast cancer.

first: Ryan

middle: T

last: Davis


title: RNA sequencing of RRM2 knockdown in C4-2 cells

summary: Human prostate cancer C4-2 cells transfected with siRNAs (siNS and siRRM2). Knockdown were confirm by westernblot or qPCR. Transfected cells were prepared for RNA-seq.

overall_design: To understand the role of RRM2 in Human prostan cencer cells. RNA sequencing were were analysed by Partek  flow


title: RNA sequencing of RRM2 overexpressing in PC-3 cells

summary: Human prostate cancer PC-3 cells stably overexpress RRM2. Overexpression of RRM2 were confirm by westernblot or qPCR. Transfected cells were prepared for RNA-seq.


title: Bulk RNAseq of A375 cells treated with Panobinostat

status: Public on Feb 19 2020

first: Lucas

last: Ferrari de Andrade

address: 1425 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

summary: The MICA and MICB genes are epigenetically regulated by HDACs. We tested if panobinostat, a broad spectrum HDAC inhibitor, affects the expression of MICA and MICB gene by a human melanoma cell line.

overall_design: Parental A375 cells were treated for 24 hours with panobinostat (50 nM) or the corresponding volume of PBS. Cells were then detached with Versene, and RNA was isolated with RNeasy Plus Mini Kit and RNase-Free DNase Set, respectively (both Qiagen kits, catalog numbers 74134 and 79254, respectively). Generation of cDNA, sequencing, and analyses were done as previously reported (Ferrari de Andrad et al, Science 2018, 359(6383)1537).


title: ChIP analysis of MADM based glioma mouse model

summary: Mosaic Analysis with Double Markers (MADM) based glioma mouse model, which homozygously lacks Tp53 and Nf1, spontaneously developed gliomas at the post-natal 90-120 days. Tp53 and Nf1 are among the most frequently mutated genes in human glioma patients. Investigating the  changes of histone modifications induced by inactivation of Tp53 and Nf1 can be a clue to clarify the mechanism of gliomagenesis. We examined the histone modifications of glioma in MADM mouse at post-natal 150 days (n=3) and post-natal 8 days (n=1) and NSC, astrocyte derived from normal mice brain (both n=1) ). We used customized SurePrint G3 Mouse GE 2×400K array slides (G4858A, Agilent Technologies).

overall_design: Microarray experiment was performed as double-color hybridization on SurePrint G3 Mouse  2 x 400K array.


title: RNA sequencing of RRM2 overexpressing in LNCaP cells

summary: Human prostate cancer LNCaP cells stably overexpress RRM2. Overexpression of RRM2 were confirm by westernblot or qPCR. Transfected cells were prepared for RNA-seq.


title: Transcriptome analysis in adipose tissues of BAF60a knockout mice

first: Siming

last: Li

department: CDB

summary:
Brown and beige fat share a remarkably similar transcriptional program that supports fuel oxidation and thermogenesis. The chromatin-remodeling machinery that governs genome accessibility and renders adipocytes poised for thermogenic activation remains elusive.
BAF60a serves an indispensable role in cold-induced thermogenesis in brown fat. Surprisingly, fat-specific BAF60a inactivation triggers more pronounced browning of inguinal white adipose tissue. These results suggest a dichotomous role of BAF60a-mediated chromatin remodeling in transcriptional control of brown and beige gene programs. To elucidate the mechanism, we performed microarray annalysis in inguinal white adipose tissues from mice after chronic cold exposure.

overall_design: Adipose-specific Baf60a knockout (AKO) and control  (flox) mice of 9 month old were subjected to either ambient temperature (RT) or chronic cold exposure (Cold). For mice under cold challenge, they went through a gradual adaptation. After reaching 10oC, the mice were maintained for another 7 days before euthanization.  Inguinal white adipose tissues were havested for RNA isolation. After quantification, equal amount of RNA from 1 or 2 mice were pooled for microarray analysis.

first: Jiandie

middle: D

last: Lin