title: Evaluation of PDE5A and PDE9A Inhibition Impacts on Cardiac mRNA Expression in a Mouse Pressure-Overload-Induced Heart Failure Model

city: Baltimore

first: Kristen

last: Kokkonen-Simon

state: Maryland

address: 720 Rutland Ave, Ross 858

department: Medicine

institute: Johns Hopkins University

summary:
Purpose: This study aimed to determine how two drugs, both ultimately activating the same effector kinase, may differentially modulate mRNA expression in a mouse model of cardiac pressure-overload-induced heart failure.
Methods: C57Bl/6J mice were subjected to sham or TAC surgeries to induce cardiac pressure-overload and subsequent heart failure. After one week, treatment with either a PDE5A inhibitor (PDE5A-I) or PDE9A inhibitor (PDE9A-I) was initiated and continued for 4 weeks, with cardiac functional measurements to assess treatment efficacy occurring weekly. At 5 weeks after surgery, mice were sacrificed and myocardium collected. Left ventricular myocardium was used for RNA isolation and subsequent mRNA sequencing on an Illumina HiSeq 2500. Data was aligned using HISAT2 v2.0.5, and transcript counts were quantified using RSEM v1.3.0. Count data was further analyzed for differential expression using Bioconductor's DESeq2 package (v1.18.1).
Results and Conclusions: Our study details how two treatments, both targeting the same kinase and with similar phenotypic improvements, result in similar pathways being altered, albeit often through modulation of different genes in the pathway. Our data demonstrates how subcellular compartmentalization of signaling pathway components can differentially impact gene expression, while still ultimately converging on similar overall effects on modification of cellular signaling.

overall_design: Myocardial mRNA profiles were generated for C57Bl6/J mice subjected to cardiac pressure-overload or sham surgeries, and concomitantly treated with either a PDE5A or PDE9A inhibitor. Sequencing was performed on an Illumina HiSeq 2500 with an n of 5-6 per group.

first: David

last: Kass


title: Marked Disparity of MicroRNA Modulation by cGMP-selective PDE5 versus PDE9 Inhibitors in Heart Disease

status: Public on Aug 09 2018

country: USA

type: Non-coding RNA profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: FOXF1 inhibits pulmonary fibrosis by preventing CDH2-CDH11 cadherin switch in myofibroblasts

city: Cincinnati

first: Yan

last: Xu

state: Ohio

address: 3333 Burnet Avenue

department: Pulmonary Biology

institute: Cicinnati children's Hospital Medical Center

summary: Idiopathic pulmonary fibrosis (IPF) is characterized by aberrant accumulation of collagen-secreting myofibroblasts.  Development of effective therapies is limited due to incomplete understanding of molecular mechanisms regulating myofibroblast expansion. FOXF1 transcription factor is expressed in resident lung fibroblasts, but its role in lung fibrosis remains unknown due to the lack of genetic mouse models. Through comprehensive analysis of human IPF genomics data, lung biopsies and transgenic mice with fibroblast-specific inactivation of FOXF1, the present study shows that FOXF1 inhibits pulmonary fibrosis. FOXF1 deletion increases myofibroblast invasion, collagen secretion, and promotes a switch from of N-cadherin (CDH2) to Cadherin-11 (CDH11), which is critical step in acquisition of pro-fibrotic phenotype. FOXF1 directly binds to Cdh2 and Cdh11 promoters and differentially regulates transcription of these genes.  Re-expression of CDH2 or inhibition of CDH11 in FOXF1-deficient cells reduces myofibroblast invasion in vitro.  FOXF1 inhibits pulmonary fibrosis by regulating a switch from CDH2 to CDH11 in lung myofibroblasts.

overall_design: RNA from fibroblasts isolated from bleomycin-treated Foxf1fl/fl and myoFoxf1 KO mouse lungs

first: Markaisa

last: Black

first: Yina

last: Du

first: Vladimir

middle: V

last: Kalinichenko

first: Tanya

last: V Kalin


title: Hepatitis B virus deregulates cell cycle to promote viral replication and a premalignant phenotype

status: Public on Aug 08 2018

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Hepatitis B virus (HBV) infection is a major health problem worldwide and chronically infected individuals are at high risk of developing cirrhosis and hepatocellular carcinoma (HCC). The molecular mechanisms whereby HBV causes HCC are largely unknown. By using a biologically relevant system of HBV infection of primary human hepatocytes (PHHs), we studied how HBV perturbs gene expressions and signaling pathways of infected hepatocytes, and whether these effects are relevant to productive HBV infection and HBV-associated HCC. Using a human growth factor antibody array, we first showed that HBV infection induced a distinct profile of growth factor production by PHHs, marked particularly by significantly lower levels of transforming growth factor (TGF)-β family of proteins in the supernatant. Transcriptome profiling next revealed multiple changes in cell proliferation and cell cycle control pathways in response to HBV infection. A human cell cycle PCR array validated deregulation of more than 20 gene associated with cell cycle in HBV-infected PHHs. Cell cycle analysis demonstrated that HBV-infected PHHs are enriched in the G2/M phase as compared to the predominantly G0/G1 phase of cultured PHHs. HBV proviral host factors, such as PPARA, RXRA and CEBPB, were up-regulated upon HBV infection and particularly enriched in cells at the G2/M phase. Together, these results support that HBV deregulates cell cycle control to render a cellular environment that is favorable for productive HBV infection. By perturbing cell cycle regulation of infected cells, HBV may coincidently induce a premalignant phenotype that predispose infected hepatocytes to subsequent malignant transformation.

overall_design: Identification of genes expressed between HBV infected positive and negative samples

first: Yuchen

last: Xia

first: Xiaoming

last: Cheng

first: Yao

last: Li

first: Kristin

last: Valdez

first: Weiping

first: T

middle: J

last: Liang


title: Bivalent chromatin domains in ovarian tumours at initial presentation identify genes predisposed to DNA hypermethylation during acquired resistance to chemotherapy [gene expression]

city: London

first: Ed

last: Curry

address: Hammersmith Hospital, Du Cane Road

country: United Kingdom

institute: Imperial College London

summary:
We have used ChIP-seq to characterize genome-wide positioning of H3K4me3 and H3K27me3 associated chromatin in primary high-grade serous ovarian carcinoma and normal ovarian surface and fallopian tube tissue. Sets of genes with proximal bivalent marks were defined using this data and subsequently evaluated as signatures of systematic change in DNA methylation and gene expression between pairs of tissue samples taken from patients at primary presentation and relapse following chemotherapy.
Gene expression microarrays from primary tumours were used to assess transcriptional associations of chromatin marks identified in tumours through ChIP-seq

overall_design: RNA was extracted from four primary tumours and hybridized to Affymetrix microarrays. For each tumour, distribution of mas5 detection calls was compared for gene sets with H3K4me3 or H3K27me3 marks.

first: E

middle: W

first: R

last: Brown


title: Common mechanism of transcription termination at coding and noncoding RNA genes in fission yeast

status: Public on Aug 10 2018

city: Sherbrooke

first: Pierre-Étienne

last: Jacques

state: Quebec

address: 2500 Boulevard de l'Université

department: Biologie

country: Canada

institute: Université de Sherbrooke

summary: Termination of RNA polymerase II (RNAPII) transcription is a fundamental step of gene expression that is critical for determining the borders between genes. In budding yeast, termination at protein-coding genes is initiated by the cleavage/polyadenylation machinery, whereas termination of most noncoding RNA (ncRNA) genes occurs via the Nrd1-Nab3-Sen1 (NNS) pathway. Unexpectedly, we show here that NNS-like transcription termination is not conserved in fission yeast. Instead, genome-wide location analyses show global recruitment of mRNA 3’ end processing factors at the end of ncRNA genes, including snoRNAs and snRNAs, and that this recruitment coincides with high levels of Ser2 and Tyr1 phosphorylation on the RNAPII C-terminal domain. We further show that termination of mRNA and ncRNA transcription requires the conserved Ysh1/CPSF-73 and Dhp1/XRN2 nucleases, supporting widespread cleavage-dependent transcription termination in fission yeast. Our findings thus reveal that a common mode of transcription termination can produce functionally and structurally distinct types of polyadenylated and non-polyadenylated RNAs.

sample_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: Exp1: Rpb1 ChIP-seq in WT and 4 NNS mutants.  Exp2: ChIP-seq of Rpb1, RNApolII CTD modifications and 3' end processing factors in WT cells.   Exp3: ChIP-seq of Rpb1 and Rpb3 in WT and dhp1-depleted cells using S. cerevisiae as spike-in.   Exp4: ChIP-seq of RNApolII CTD modification in WT and dhp1-depleted cells using S. cerevisiae spike-in.  Exp5: ChIP-seq of Rpb1 in WT and ysh1-depleted cells using S. cerevisiae as spike-in

first: Marc

last: Larochelle

first: Marc-Antoine

last: Robert

first: François

last: Bachand


title: Role for TNFAIP2: Relationships with Outcomes and EMT in Urothelial Cancers under the Control of Cisplatin

city: Tokyo

first: Naoya

last: Niwa

address: 35, Shinanomachi, Shinjuku-ku

country: Japan

institute: Keio University School of Medicine

summary: Background: Cisplatin (CDDP)-based chemotherapy is the gold standard treatment for many cancer types. However, the phenotypic hallmark of tumors often changes after CDDP, with the acquisition of Epithelial-to-mesenchymal transition (EMT) and platinum resistance. Yet, the mechanisms by which cancer cells acquire EMT under the control of CDDP remain unclear.  Methods: Following an investigation of urothelial cancers (UCs) before and after the acquisition of platinum resistance, we offered the new target TNFAIP2, which led to EMT and tumor invasion. TNFAIP2 expression in cancers were examined at the protein and transcription levels.  Results: Clinically, up-regulated TNFAIP2 expression was identified as a significant predictor of mortality in upper urinary tract UCs. TNFAIP2 knockdown resulted in up-regulated E-cadherin expression and down-regulated TWIST expression in cancers, which decreased motile function. TNFAIP2 overexpression led to down-regulated E-cadherin expression and up-regulated TWIST expression. Clinical investigations on matched pre- and post-CDDP-treated sections confirmed up-regulated TNFAIP2 expression in CDDP-treated tumors, but down-regulated E-cadherin expression. A global gene expression analysis following TNFAIP2 knockdown identified MTDH as a positive regulator of TNFAIP2-derived EMT acquisition.   Conclusions: Our results suggest a relationship between TNFAIP2 and EMT in cancers, in which MTDH expression levels in cancer cells are vital for promoting TNFAIP2-derived EMT acquisition.

overall_design: To investigate the relationship between TNFAIP2 and EMT, we compared changes in global gene expression between before and after the knockdown of TNFAIP2 in platinum-resistant 5637PR cells.

first: Nobuyuki

last: Tanaka

first: Hiroshi

last: Hongo

first: Yasumasa

last: Miyazaki

first: Ryuichi

last: Mizuno

first: Eiji

last: Kikuchi

first: Shuji

last: Mikami

first: Takeo

last: Kosaka

first: Mototsugu

last: Oya


title: Bivalent chromatin domains in ovarian tumours at initial presentation identify genes predisposed to DNA hypermethylation during acquired resistance to chemotherapy [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: H3K4me3 and H3K27me3 ChIP-seq on Serous epithelial ovarian carcinoma, Normal ovarian surface epithelium and Normal fallopian tube epithelium.


title: Cancer associated mRNAs regulated by the Helix Loop Helix motif of human EIF3A

city: Berkeley

first: Marina

last: Volegova

state: CA

address: 748 Stanley Hall, MS 3220

department: Molecular and Cell Biology

institute: University of California - Berkeley

summary: Improper regulation of translation initiation, a vital check-point of protein synthesis in the cell, has been linked to a number of cancers. Overexpression of protein subunits of eukaryotic translation initiation factor 3 (eIF3) has been associated with increased translation of mRNAs involved in cell proliferation. In addition to playing a major role in general translation initiation by serving as a scaffold for the assembly of translation initiation complexes, eIF3 regulates translation of specific cellular mRNAs and viral RNAs. Mutations in the N-terminal Helix-Loop-Helix (HLH) RNA-binding motif of the EIF3A subunit in eIF3 interfere with Hepatitis C Virus Internal Ribosome Entry Site (IRES) mediated translation initiation in vitro. Here we use RNA-seq and ribosome profiling of engineered lentiviral HEK293T cells to show that the EIF3A HLH motif controls translation of a small set of cellular transcripts enriched in oncogenic mRNAs, including MYC.

overall_design: Ribosome profiling and RNA-seq analysis of control and EIF3A triple mutant HEK293T cells in biological triplicates.

first: Jamie

middle: H

last: Cate


title: Evaluation of PDE5A and PDE9A Inhibition Impacts on Cardiac microRNA Expression in a Mouse Pressure-Overload-Induced Heart Failure Model

first: Kristen

last: Kokkonen-Simon

summary:
Purpose: This study aimed to determine how two drugs, both ultimately activating the same effector kinase, may differentially modulate microRNAs in a mouse model of cardiac pressure-overload-induced heart failure.
Methods: C57Bl/6J mice were subjected to sham or TAC surgeries to induce cardiac pressure-overload and subsequent heart failure. After one week, treatment with either a PDE5A inhibitor (PDE5A-I) or PDE9A inhibitor (PDE9A-I) was initiated and continued for 4 weeks, with cardiac functional measurements to assess treatment efficacy occurring weekly. At 5 weeks after surgery, mice were sacrificed and myocardium collected. Left ventricular myocardium was used for RNA isolation and subsequent microRNA sequencing on an Illumina HS2500. Data was analyzed using the miRge program (v1.0), which utilizes CutAdapt 1.8 to pre-process sequencing data and Bowtie 1.1.1 to perform read alignments, to generate miRNA counts and reads-per-million data. Count data was further analyzed for differential expression using Bioconductor's DESeq package (v1.26.0).
Results and Conclusions: Our study details how two treatments, both targeting the same kinase and with similar phenotypic improvements, result in profoundly different miRNA expression profiles. We found that PDE5A inhibition greatly decreased microRNA expression as compared to heart failure controls, whereas PDE9A inhibition changed virtually no microRNAs in comparison. Our results illustrate how cellular compartmentalization of enzymes can play a significant role in microRNA modulation, as well as a disconnect between phenotypic outcome and microRNA profile, despite treatments impacting the same effector kinase and being equally effective in ameliorating disease.

overall_design: Myocardial microRNA profiles were generated for C57Bl6/J mice subjected to cardiac pressure-overload or sham surgeries, and concomitantly treated with either a PDE5A or PDE9A inhibitor. Sequencing was performed on an Illumina HiSeq 2500 with an n of 5-6 per group.

first: David

last: Kass


title: Single cell RNA-seq study of wild type and Hox mutant developing uterus

status: Public on Aug 07 2018

first: Mike

last: Adam

address: 240 Albert Sabin Way

department: CBDI

institute: Cincinnati Children's Hospital Research Foundation

summary: This study identifies a novel role for the Hoxc9,10,11 genes in uterine gland formation. This function is redundant with the Hoxa9,10,11 and Hoxd9,10,11 genes and is only seen in a sensitized genotype with reduced expression of these paralogs. We further used scRNA-seq to define the gene expression patterns of the multiple cell types of the developing uterus. The results define the gene expression patterns driving lineage specific development. In addition scRNA-seq was used to characterize the perturbed gene expression levels of all developing uterus cell types in the ACD+/- and ACD+/-WTA11 mutants. Particularly striking was the reduced Wnt signaling and the disruption of the Cxcl12/Cxcr4 axis in the mutants.

overall_design: Using droplet RNA sequencing, transcriptomes of single cells from wild-type and Hox mutant mouse uteri were analyzed

first: Robert

last: Mahoney

first: Michael

middle: L

last: Mucenski

first: Steve

last: Potter


title: A compendium of conserved cleavage and polyadenylation events in mammalian genes

city: Newark

first: Bin

last: Tian

state: NJ

address: 205 South Orange Ave.

department: Department of Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers New Jersey Medical School

summary: Cleavage and polyadenylation is essential for 3’ end processing of almost all eukaryotic mRNAs. Recent studies have shown widespread alternative cleavage and polyadenylation (APA) events leading to mRNA isoforms with different 3’UTRs and/or coding sequences. Here we present a compendium of conserved cleavage and polyadenylation sites (PASs) in mammalian genes, based on ~1.2 billion 3’ end sequencing reads from over 360 human, mouse and rat samples. We show that ~80% of mammalian mRNA genes contain at least one conserved PAS, and ~50% have conserved APA events. PAS conservation generally reduces promiscuous 3’ end processing, stabling gene expression levels across species. Conservation of APA correlates with gene age, gene expression features, and gene functions. Genes with certain functions, such as cell morphology, cell proliferation, and mRNA metabolism, are particularly enriched with APA events. While tissue-specific genes typically have a low APA rate, brain-specific genes tend to evolve APA. We show enrichment of mRNA destabilizing motifs in alternative 3’UTR sequences, leading to substantial differences in mRNA stability between 3’UTR APA isoforms. Using conserved PASs, we reveal sequence motifs surrounding APA sites and a preference of adenosine at the cleavage site. Mutations of the U-rich motif around the PAS often accompany APA profile changes between species. Analysis of lncRNA PASs indicates a mechanism of PAS fixation involving evolution of A-rich motifs. Taken together, our results present a comprehensive view of PAS evolution in mammals, and a phylogenic understanding of APA functions.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design:
21 3'READS libraries for the analysis of APA in heart, testis and heart between mouse and rat

107 3'READS human samples used in PolyA_DB version 3.2

first: Ruijia

last: Wang

first: Dinghai

last: Zheng

first: Ghassan

last: Yehia


title: Transcriptome analysis of mesenchymal CSC-like cells harboring mutant p53

city: Rehovot

first: Dan

last: Ben-Avraham

address: Herzl 234

department: G-INCPM

country: Israel

institute: Weizmann Institute of Science

summary: We show that mesenchymal CSC-like cells express an embryonic stem cell signature that is mutant p53 dependent

overall_design: Examination of three p53 mutant mesenchymal stem cells and ten derived CSC-like cell lines and 2 derived p53 mutant KO clones compared to control clones

first: Rotter

last: Varda


title: ATAC sequencing of sorted BCC cells after vismodegib treatment

city: South San Francisco

last: Piskol

address: 1 DNA Way

department: gRED Computational Sciences

institute: Genentech Inc.

summary:
K14Cre-ER; Ptch1fl/fl; p53fl/fl;Lgr5GFP mice were aged until the appropriate tumor density was achieved. Skin samples were taken from control mice (untreated) or mice treated for 6 days or 14 days at twice a day dosing with vismodegib (75mg/kg body weight). RNA was extracted from freshly FACS sorted tumor cells based on GFP intensity.
The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech.

overall_design: Chromatin accessibility profiling of tumor cells from BCC mice sorted at 6 days and 14 days of vismodegib treatment compared to sorted tumor cells from untreated mice.

first: Brian

last: Biehs


title: Hedgehog gradient in the stroma maintains niche diversity and organ function [scRNA-seq]

city: San Francisco

first: Peng

last: Tien

address: 513 Parnassus Ave, Health Sciences East 1350

department: Department of Pulmonary Medicine

institute: University of California San Francisco

summary: Two single-cell transcriptional analyses were performed on adult human lung distal and proximal stromal cells, respectively. We isolated lung specimen from both the proximal portion enriched in airways and distal portion enriched in alveoli separately. The lung fragments were then dissociated to single cells and FACSorted for stromal cells based on negative expression of epithelial, hematopoietic, and endothelial markers (EPCAM-/CD45-/CD11b-/CD31-). Library preparation was performed separately for the proximal and distal-derived stromal cells so that each subset has distinctive barcodes to determine anatomical origin, and approximately 10,000 cells were captured from each specimen. The results demonstrate that the proximal and distal human lung stromal subsets demonstrate significant overlap of homologous genes with their murine counterparts generated from Gli2+ murine stroma single-cell transcriptional analysis.

overall_design: We isolated the adult human lung specimen from both the proximal portion enriched in airways and distal portion enriched in alveoli separately. Then the lung tissues were dissociated to single cells, stained with anti-CD45-APC-Cy7, anti-CD11b-APC-Cy7, anti-CD31-APC-Cy7 and anti-Epcam-APC-Cy7 and DRAQ7, and subjected to FACS to select live stromal cells. Doublets and dead cells were excluded based on forward scatter, side scatter and DRAQ7 fluorescence. The hematopoietic cells were excluded by stained with anti-CD45-APC-Cy7 and anti-CD11b-APC-Cy7, the endothelial cells were excluded by stained with anti-CD31-APC-Cy7, and the epithelial cells were excluded by stained with anti-Epcam-APC-Cy7. Then the stromal cells were sorted and prepared using the 10X single cell instrument and v1 10X single cell kits according to standard protocol. Single cell sequencing of adult human lung stromal populations were performed by using the HiSeq2500.

first: Chaoqun

first: Tien

last: Peng


title: Molecular profiling reveals immunogenic cues in anaplastic large cell lymphomas with DUSP22 rearrangements

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

institute: Mayo Clinic

summary: Anaplastic large cell lymphomas (ALCLs) are CD30-positive T-cell non-Hodgkin lymphomas broadly segregated into ALK-positive and ALK-negative types.  While ALK-positive ALCLs consistently bear rearrangements of the ALK tyrosine kinase gene, ALK-negative ALCLs are clinically and genetically heterogeneous.  About 30% of ALK-negative ALCLs have rearrangements of DUSP22 and have excellent long-term outcomes with standard therapy.  To better understand this group of tumors, we evaluated their molecular signature using gene expression profiling.  DUSP22-rearranged ALCLs belonged to a distinct subset of ALCLs that lacked expression of genes associated with JAK-STAT3 signaling, a pathway contributing to growth in the majority of ALCLs.  Reverse-phase protein array and immunohistochemical studies confirmed the lack of activated STAT3 in DUSP22-rearranged ALCLs.  DUSP22-rearranged ALCLs also overexpressed immunogenic cancer-testis antigen (CTA) genes and showed marked DNA hypomethylation by reduced representation bisulfate sequencing and DNA methylation arrays.  Pharmacologic DNA demethylation in ALCL cells recapitulated the overexpression of CTAs and other DUSP22 signature genes.  Additionally, DUSP22-rearranged ALCLs minimally expressed PD-L1 compared to other ALCLs, but showed high expression of the costimulatory gene CD58 and HLA class II.  Taken together, these findings indicate that DUSP22 rearrangements define a molecularly distinct subgroup of ALCLs and that immunogenic cues related to antigenicity, costimulatory molecule expression, and inactivity of the PD-1/PD-L1 immune checkpoint likely contribute to their favorable prognosis.  More aggressive ALCLs might be pharmacologically reprogrammed to a DUSP22-like, immunogenic molecular signature through the use of demethylating agents and/or immune checkpoint inhibitors.

overall_design: 31 frozen ALCL biopsies were collected fro humans and subjected to gene expression analysis using Affymetrix arrays

first: Rebecca

last: Boddicker

first: Naoki

last: Oishi

first: Martin

middle: B

last: Pedersen

first: Guangzhen

last: Hu

first: Karen

last: Rech

first: Rhett

middle: P

last: Ketterling

first: Jagmohan

last: Sidhu

first: Xueju

first: Ryohei

last: Katoh

first: Ahmet

last: Dogan

first: Sertac

last: Kip

first: Julie

middle: M

last: Cunningham

first: Zhifu

last: Sun

first: Saurabh

last: Baheti

middle: C

last: Porcher

first: Jonathan

last: Said

first: Liuyan

last: Jiang

first: Stephen

last: Hamilton-Dutoit

last: Møller

first: Peter

last: Nørgaard

first: N

middle: N

last: Bennani

first: Wee-Joo

last: Chng

first: Gaofeng

last: Huang

middle: K

last: Link

first: Fabio

last: Facchetti

first: James

middle: R

last: Cerhan

first: Francesco

last: d'Amore

last: Ansell

first: Andrew

last: Feldman


title: Generation of trichogenic adipose-derived stem cells by expression of three factors

city: Incheon

first: Nahyun

last: Choi

state: Incheon

address: gwahackro 85

department: college of pharmacology

country: South Korea

institute: Yonsei University

summary:
Background: Previous studies demonstrated that adipose-derived stem cells (ASCs) can promote hair growth, but unmet needs exist for enhancing ASC hair inductivity.
Objective: Therefore, we introduced three trichogenic factors platelet-derived growth factor-A, SOX2, and β-catenin to ASCs (tfASCs) and evaluated whether tfASCs have similar characteristics as dermal papilla (DP) cells.
Method: Global gene expression was examined using NGS analysis. Telogen-to-anagen induction, vibrissae hair follicle organ culture and patch assay were used.
Results: tfASC cell size is smaller than that of ASCs, and they exhibit short doubling time. tfASCs also resist aging and can be expanded until passage 12. Cell proportion in S and G2/M increases in tfASCs, and tfASCs express high mRNA levels of cell cycle related genes. The mRNA expression of DP markers was notably higher in tfASCs. Moreover, NGS analysis revealed that the global gene expression of tfASCs is similar to that of DP cells. The  injection of tfASCs accelerated the telogen-to-anagen transition and conditioned medium of tfASCs increased the anagen phase of vibrissal hair follicles. Finally, we found that the injection of 3D-cultured tfASCs at p 9 generated new hair follicles in nude mice.
Conclusion: Collectively, these results indicate that 1) tfASCs have similar characteristics as DP cells, 2) tfASCs have enhanced hair-regenerative potential compared with ASCs, and 3) tfASCs even at late passage can make new hair follicles in a hair reconstitution assay. Because DP cells are difficult to isolate/expand and ASCs have low hair inductivity, tfASCs and tfASC-CM are clinically good candidates for hair regeneration.

overall_design:
NGS analysis was carried out using RNA from ASCs, tfASCs and DP cells.
----------------------
contributor: MACROGEN


title: Single-Cell Transcriptomes Distinguish Stem Cell State Changes and Lineage Specification Programs in Early Mammary Gland Development

city: LA JOLLA

first: Rajshekhar

last: Giraddi

state: California

address: 10010 north torrey pines road, Wahl Lab Salk Institute

department: Gene Expression Laboratory

institute: Salk Institute of Biological Sciences

summary: Single cell analysis of the mouse mammary gland from embryonic to adult stages using 10X Chromium platform.

overall_design:
Dissociated cells processed using 10X protocol and sequenced on Illumina

All information on 10X website to decode the sequence and barcodes at;
https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger

The analysis is often done on the freely available Cell Ranger software previded by 10X Genomics Inc but using the information on the website, it can be run independently without using the website.
Please contact the submitter for the codes/instructions to run this on R

Please note that the analysis was carried out similar to PMID:29144463 [doi:10.1038/nature24489]

first: Chi-Yeh

last: Chung

first: Richard

middle: E

last: Heinz

first: Ozlen

last: Balcioglu

first: Mark

last: Novotny

first: Christy

last: Trejo

first: Christopher

last: Dravis

first: Berhane

last: Hagos

first: Elnaz

last: Mehrabad

first: Luo

last: Rodewald

first: Jae

last: Hwang

first: Cheng

last: Fan

first: Roger

last: Lasken

first: Katherine

middle: T

last: Varley

first: Charles

last: Perou

first: Geoffrey

last: Wahl

first: Benjamin

last: Spike


title: Deep sequencing analyzed the coverage of sgRNA in haploid stem cells.

status: Public on Aug 06 2018

city: Shanghai

first: Qing

last: Li

address: 320 Yueyang Road

department: institute of biochemistry and cell biology

country: China

institute: Chinese Academy of Science

summary: We used the deep sequencing to analyze the sgRNA coverage of Dnd1 library in 4B2N1-DP1 and 4B2N1-DP2 cell lines. The amplicon obtained from PCR reaction from genome using high-fidelity DNA polymerase. By obtaining over 10 million reads of each sample from deep sequencing, we mapped the reads to the reference sequence and then calculated coverage and counts. The results showed that the hit number of different sgRNAs were variable

overall_design: Deep sequencing analyzed two different cell lines.

first: Li

last: Jinsong

last: Qing


title: Whole exome sequencing analyzed the off-target effect of gene editing through BE3 system.

type: Genome variation profiling by high throughput sequencing

summary: We used the whole exome sequencing to analyze the off-target effect of base editing system in mouse genomic DNA, which was extracted from haploid stem cells, mouse tails of semi-cloned embryos and mutant pups. The purpose of this sequencing is to find whether there exists off-target effect in the genome. By obtaining over 100 million reads of each sample from WES, we mapped the reads to the reference data base (mm10) and calculated the numbers of SNVs and indels. After filtering out naturally-occurring variants in the SNP database (dbSNP) and excluding SNPs also found in the wild-type genome, we next compared the DNA sequences at the remaining SNP sites with the on-target sequence. The results indicated that rare off-targets events happened in tested cell and embryos.

overall_design: The off-target effect of 5 different sgRNAs in 11 different edited cell and tissue samples and 3 control samples.


title: Life-threatening influenza pneumonitis in a child with inherited IRF9 deficiency

city: Doha

first: Tanwir

last: Habib

address: Al Luqta Street

country: Qatar

institute: Weill Cornell Medicine Qatar

summary: Life-threatening pulmonary influenza can be caused by inborn errors of type I and III IFN immunity. We report a 5 year-old child with severe pulmonary influenza at 2 years. She is homozygous for a loss-of-function IRF9 allele. Her cells activate gamma-activated factor (GAF) STAT1 homodimers but not interferon-stimulated gene factor 3 (ISGF3) trimers (STAT1/STAT2/IRF9) in response to IFN-α2b. The transcriptome induced by IFN-α2b in the patient’s cells is much narrower than that of control cells; however, induction of a subset of interferon-stimulated gene transcripts remains detectable. In vitro, the patient’s cells do not control three respiratory viruses, influenza A virus (IAV), parainfluenza virus, and respiratory syncytial virus. These phenotypes are rescued by wild-type IRF9, whereas silencing IRF9 expression in control cells increases viral replication. However, the child has controlled various common viruses in vivo, including respiratory viruses other than IAV. Our findings show that human IRF9- and ISGF3-dependent type I and III IFN responsive pathways are essential for controlling IAV.

overall_design: Total of 72 samples, 38 samples from primary fibroblasts and 34 samples from EBV-transformed B cells, were analyzed using paired-end RNA sequence data. Out of 38 samples from primary fibroblasts, 3 control samples are paired with no stimulation vs IFNa2b stimulation. Out of 34 samples from B-cells, 3 control samples are paired with no stimuliion vs IFNa2b stimulation. In addition to healthy control subjects, patients with AR complete STAT1 (STAT1 -/-) or STAT2 (STAT2 -/-) deficiency were analyzed for comparison.

first: Nicholas

last: Hernandez

first: Isabelle

last: Melki

first: Huie

last: Jing

first: Susie

last: Huang

first: Jeffrey

last: Danielson

first: Tomasz

last: Kula

first: Scott

last: Drutman

first: Serkan

last: Belkaya

first: Vimel

last: Rattina

first: Lazaro

last: Lorenzo-Diaz

first: Anais

last: Boulai

first: Yoann

last: Rose

first: Naoki

last: Kitabayashi

first: Mathieu

last: Rodero

first: Cecile

last: Dumaine

first: Stéphane

last: Blanche

first: Marie-Noëlle

last: Lebras

first: Man

last: Leung

first: Lisa

middle: S

last: Mathew

first: Bertrand

last: Boisson

first: Shen-Ying

last: Zhang

first: Stephanie

last: Boisson-Dupuis

first: Damien

last: Chaussabel

first: Luigi

middle: D

last: Notarangelo

first: Stephen

last: Elledge

first: Michael

last: Ciancianelli

first: Laurent

last: Abel

first: Qian

first: Nico

last: Marr

first: Yanick

last: Crow

first: Helen

last: Su

first: Jean-Laurent

last: Casanova


title: Single-cell RNA-seq of spiral ganglion neurons from wildtype and Vglut3-/- mice

city: Boston

last: Goodrich

state: MA

address: 220 Longwood Avenue

department: Neurobiology

institute: Harvard Medical School

summary: Molecular heterogeneity among spiral ganglion neurons (SGNs) in the mouse cochlea was investigated in two genetic backgrounds: 1) wildtype, 2) Vglut3-/-, which lack inner hair cell-driven glutamatergic activation of SGNs.

overall_design: Individual spiral-ganglion neurons expressing the fluorescent reporter tdTomato were dissociated and manually placed into PCR tubes; single-cell libraries were made by the Smart-seq2 approach; sequencing was done using the NextSeq platform (Illumina) at an average read depth of 4.5 million; bioinformatic analysis was conducted in R. Genotypes: bhlhb5::cre/+; Ai14/+ (wildtype) and bhlhb5::cre/+;Ai14/+; Vglut3-/-  (Vglut3-/-). Age: P25-P27

first: Brikha

last: Shrestha


title: Bivalent chromatin domains in ovarian tumours at initial presentation identify genes predisposed to DNA hypermethylation during acquired resistance to chemotherapy

first: Ed

last: Curry

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

overall_design: Refer to individual Series


title: Cytoplasmic NPM1 maintains the leukemic state through HOX expression

city: Houston

last: Gundry

state: Texas

address: One Baylor Plaza, N1030

department: Department of Pediatrics

institute: Baylor College of Medicine


title: ATAC sequencing of HAP1 cells

status: Public on Aug 05 2018

city: Oslo

first: Roza Berhanu

last: Lemma

address: Blindernveien 31

department: Department of Biosciences

country: Norway

institute: University of Oslo

summary: We analysed the global effect of CHD3-KO and SENP1-KO HAP1 cell lines compared to control cell line, on chromatin accessibility using ATAC-seq.

overall_design: CRISPR-Cas9-generated knockout cells for CHD3 and SENP1 in HAP1 cells were assayed by ATAC-seq, where 150,000 cells were harvested to investigate changes in chromatin accessibility. Three individual experiments were performed. Libraries were prepared and 40-bp paired-end reads were obtained using an Illumina Nextseq 500 sequencer.

first: Odd

last: Gabrielsen

first: Roza


title: Processing of eukaryotic Okazaki fragments by redundant nucleases can be uncoupled from ongoing DNA replication in vivo

status: Public on Aug 04 2018

city: New York

first: Duncan

last: Smith

state: NY

address: 1009 Silver Center, 100 Washington Sq E

department: Dept. of Biology/Center for Genomics and Systems Biology

institute: New York University

summary: Prior to ligation, each Okazaki fragment synthesized on the lagging strand in eukaryotes must be nucleolytically processed. Nuclease cleavage takes place in the context of 5’ flap structures generated via strand-displacement synthesis by DNA polymerase delta. At least three DNA nucleases: Rad27 (Fen1), Dna2, and Exo1, have been implicated in processing Okazaki fragment flaps. However, neither the contributions of individual nucleases to lagging-strand synthesis nor the structure of the DNA intermediates formed in their absence have been clearly defined in vivo. By conditionally depleting lagging-strand nucleases and directly analyzing Okazaki fragments synthesized in vivo in S. cerevisiae, we conduct a systematic evaluation of the impact of Rad27, Dna2 and Exo1 on lagging-strand synthesis. We find that Rad27 processes the majority of lagging-strand flaps, with a significant additional contribution from Exo1 but not from Dna2. When nuclease cleavage is impaired, we observe a reduction in strand-displacement synthesis as opposed to the widespread generation of long Okazaki fragment 5’ flaps, as predicted by some models. Further, using cyclin-controlled constructs, we demonstrate that both the nucleolytic processing and the ligation of Okazaki fragments can be uncoupled from DNA replication and delayed until after synthesis of the majority of the genome is complete.

overall_design: Okazaki fragments from asynchronous yeast cultures were enriched by conditional depletion of Cdc9 , and processed into strand-specific libraries for paired-end high-throughput sequencing. We analyzed Okazaki fragment size, terminus location and ligatability in nuclease mutants, with two biological replicates each.

first: Malik

last: Kahli

first: Joseph

last: Osmundson

first: Rani

last: Yeung


title: A Time-resolved Multi-omic Atlas of the Developing Mouse Stomach

city: Beijing

first: Xianju

last: Li

address: Life Science Park Road 38#

institute: National Center for Protein Sciences (The PHOENIX Center, Beijing)

summary: The mouse stomach secrets digestive enzymes and stomach acid, and plays a key role in food digestion. While there are a few studies on the morphological changes during the stomach development, a comprehensive, systematic omics study is still missing. Here, we present a comprehensive, temporal proteome atlas of the mouse stomach by sequential mapping stomach tissues at multiple developmental stages. The quantitative analysis of 12,108 gene products provides coverage sufficient to observe the protein dynamics of the developing stomach. The whole process of stomach development can be roughly divided into three phases according to changes of RNAs or proteins. The molecular functions of protein modules pinpoint the gain of stomach functions at the longitudinal scale. Dissection of 8 key signaling pathways identified master regulators in governing stomach development and gastric cancer. Remarkably, many proteins differentially expressed in stomach development are also significantly overexpressed in diffuse-type gastric cancer, suggesting a close correlation between development and tumorigenesis. The transcriptome of the developing stomach reveals functionally important isoforms relevant to development. When combined with the proteomes, several functionally unannotated novel splicing junction transcripts were identified and validated at the peptide level. Overall, our study provides a valuable resource to understand stomach development and its connection to gastric cancer.

overall_design: We collected 3 replicates at proteome level and one replicates at transcriptome level of whole stomach organs at 15 time points that covered embryonic days (E12.5, E13.5, E14.5, E15.5, E16.5, E17.5, E18.5), postnatal days (D1, D3, D5), and postnatal weeks (W1, W2, W3, W6, W8).

first: Chunchao

last: Zhang

first: Tongqing

last: Gong


title: Comparative expression data between tumor epithelium of APCmin/+ FSPCre-PPARB -/- and PPARB flox/flox

city: Singapore

first: Eddie

middle: Han Pin

last: Tan

address: 60 Nanyang Drive

department: School of Biological Sciences

country: Singapore

institute: Nanyang Technological University

summary:
Stroma secretes complex regulatory signals, including reactive oxygen species, that are involved in mediating cancer development. Ablation of PPARB expression in fibroblastic cells results in modulation of oxidative stress signals that lead
By means of gene expression analysis, we seek to identify key gene expression changes in tumor epithelial cells between FSPCre-PPARB -/- and PPARB flox/flox mice.

overall_design:
Expression profiling of  FSPCre-PPARB KO tumor epithelium, FSPCre-PPARB KO tumor adjacent epithelium, PPARB floxed tumor epithelium, PPARB floxed tumor adjacent epithelium.
Intestines were harvested from 25 week old mice on C57BL6/J APCmin/+ backgrounds and prepared for histological staining. Tumor and tumor adjacent epithelium were microdissected from stained histological slides using Zeiss PALM III laser disection microscope.


title: Genotype-by-environment-by-environment interactions in the Saccharomyces cerevisiae transcriptomic response to alcohols and anaerobiosis

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

summary: Gene expression in budding yeast responding to alcohols with and without oxygen

overall_design: RNA-seq in individual strains growing in different conditions

first: Maria

last: Sardi


title: Next Generation Sequencing Facilitates Quantitative Analysis of Normoxia/Hypoxia  Human Dental Pulp Cells Transcriptomes

status: Public on Aug 03 2018

city: Guangzhou

first: Fei

last: Liu

address: No. 1838 North Guangzhou Avenue

institute: Southern Medical University

summary: We report the application of high-throughput profiling of gene expression in human dental pulp cells under normoxia and hypoxia conditions.

overall_design: Examination of hypoxia induced molecular changes in human dental pulp cells.

first: Zhenhua

last: Luo


title: Cytoplasmic NPM1 maintains the leukemic state through HOX expression [RNA-seq]

first: Michael

summary: NPM1 is the most frequently mutated gene in cytogenetically normal acute myeloid leukemia (AML). In AML cells, NPM1 mutations result in abnormal cytoplasmic localization of the mutant protein (NPM1c). NPM1 mutations are founding genetic lesions, however it is unknown whether NPM1c is required to maintain the leukemic state. Here, we show that loss of NPM1c from the cytoplasm, either through nuclear relocalization or targeted degradation, results in downregulation of homeobox (HOX) genes, and differentiation and cell growth arrest of AML cells. Additionally, we show that HOX downregulation is the earliest transcriptional event following the loss of NPM1c from the cytoplasm, preceding and promoting differentiation. Finally, we show that XPO1 inhibition efficiently relocalizes NPM1c to the nucleus, enables differentiation and prolongs survival of Npm1c+ leukemic mice. We describe an exquisite dependency of NPM1-mutant AML cells on NPM1c, providing the rationale for the use of nuclear export inhibitors in AML with mutated NPM1.

overall_design: Examination of transcriptional and epigenetic changes upon nuclear relocalization or targeted degradation of NPM1c.

first: Lorenzo

last: Brunetti


title: Functional aspects of meningeal lymphatics in ageing and Alzheimer's disease [3 of 3]

city: Charlottesville

first: Christopher

last: Overall

state: Virginia

address: 409 Lane Road

department: Neuroscience

institute: University of Virginia

summary: Aging is a major risk factor for many neurological pathologies, including Alzheimer’s disease (AD). However, the mechanisms underlying brain aging and cognitive decline remain elusive. Body tissues are perfused by interstitial fluid (ISF), which is locally reabsorbed via the lymphatic vascular network. In contrast, the parenchyma of the central nervous system (CNS) is devoid of lymphatic vasculature; in the brain, removal of cellular debris and toxic molecules, such as amyloid beta (A) peptides, is mediated by a combination of transcellular mechanisms of transport across the blood−brain and blood−cerebrospinal fluid (CSF) barriers, phagocytosis and digestion by resident microglia and recruited monocytes/macrophages, and CSF influx and ISF efflux through a paravascular route. The recent characterization of meningeal lymphatic vessels prompted a reassessment of the conventional pathways of CNS waste clearance. The role of this vasculature in brain function, specifically in the context of aging and AD, is still poorly understood. Here we show that meningeal lymphatic vessels play an essential role in maintaining brain homeostasis by draining macromolecules from the CNS (CSF and ISF) into the cervical lymph nodes. Using pharmacological, surgical, and genetic models we show that impairment of meningeal lymphatic function in adult mice slows paravascular influx of CSF macromolecules and efflux of ISF macromolecules, and induces cognitive impairment. Treatment with a lymphangiogenic factor, vascular endothelial growth factor C (VEGF-C), enhances meningeal lymphatic drainage of CSF macromolecules, improving brain perfusion and learning and memory performance in aged mice. Disruption of meningeal lymphatic vessels in transgenic mouse models of AD promotes amyloid deposition in the meninges, which closely correlates with human meningeal pathology, and aggravates overall disease severity. Our findings suggest that meningeal lymphatic dysfunction may be an aggravating factor in AD pathology and in age-associated cognitive decline. Thus, augmentation of meningeal lymphatic function might be a promising therapeutic target for preventing or delaying age-associated neurological diseases.

overall_design: Male C57BL/6J mice (2 months-old) were injected (intra-cisterna magna) with Visudyne (verteporfin for injection), or vehicle as control, and submitted to a step of photoconversion, to induce meningeal lymphatic vessel ablation. This procedure was repeated 2 weeks later to ensure prolonged meningeal lymphatic dysfunction. 2 weeks after the last surgical procedure, whole hippocampus was macrodissected and total RNA was extracted for sequencing.

first: Sandro

last: Da Mesquita

first: Antoine

last: Louveau

first: Andrea

last: Vaccari

first: Igor

last: Smirnov

first: R

last: Cornelison

first: Kathryn

last: Kingsmore

first: Christian

last: Contarino

first: Suna

last: Onengut-Gumuscu

first: Emily

last: Farber

first: Daniel

last: Raper

first: Kenneth

last: Viar

first: Romie

last: Powell

first: Wendy

last: Baker

first: Nisha

last: Dabhi

first: Robin

last: Bai

first: Rui

last: Cao

first: Song

last: Hu

first: Stephen

last: Rich

first: Jennifer

last: Munson

first: M

last: Lopes

first: Scott

last: Acton

first: Jonathan

last: Kipnis


title: MPTAC determines APP fragmentation via sensing sulfur amino acid catabolism

city: Kansas City

first: Madelaine

last: Gogol

state: MO

address: 1000 E. 50th Street

department: Computational Biology Core

institute: Stowers Institute

summary: The data from the analysis of transcripts of metabolic enzymes suggested the metabolic pathways that are directly/indirectly regulated by MPTAC. The transcript data also supports the metabolomics data, which suggested the connection of metabolic pathways regulated by MPTAC.  The analysis of junction reads led to the discovery of involvement of MPTAC in splicing regulation.

overall_design: 3 replicates of control and 3 of knockdown MOCS2 in human embryonic kidney cells

first: Tamaki

last: Suganuma


title: RNA-seq of Adult Mouse Pillar and Deiters Supporting Cells, Inner and Outer Hair Cells of the Organ of Corti

city: Omaha

first: David

middle: ZZ

last: He

state: Nebraska

address: 2500 California Plaza

department: Biomedical Sciences

institute: Creighton University


title: Cytoplasmic NPM1 maintains the leukemic state through HOX expression [ChIP-seq]

first: Michael

last: Gundry

first: Lorenzo

last: Brunetti


title: RNA-sequencing of Adult Mouse Pillar and Deiters’ Supporting Cells of the Organ of Corti

summary: To understand the basic biological properties of supporting cells of the mammalian inner ear, we examined the transcriptome of adult pillar and Deiters’ cells. Morphologically distinct pillar and Deiters’ cells were isolated from the organ of Corti from adult CBA/J mice. One thousand pillar and Deiters’ cells were separately collected for each biological replicate, using the suction pipette technique. RNA sequencing of three biological replicates, each with two technical repeats, was performed. The resulting sequenced reads were mapped. Comparisons between pillar cells and Deiters’ cells allow identification of enriched genes, as well as differentially expressed genes that result in cellular specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology, function, and pathology of adult mouse pillar and Deiters’ cells.

overall_design: One thousand pillar cells and 1,000 Deiters’ cells were separately collected for each biological replicate, using the suction pipette technique. RNA sequencing of three biological replicates for the two cell types was performed. The resulting sequenced reads were mapped. Comparisons between pillar cells and Deiters’ cells allow identification of enriched genes which may underlie cell specialization

first: Huizhan

last: Liu

first: Lei

last: Chen

first: Kimberlee

last: Giffen

first: Sean

last: Stringham

first: Yi

last: Li

first: Paul

last: Judge

first: Kirk

last: Beisel

middle: Z


title: RNA-seq profiling of a mouse B cell lymphoma cell line treated with the KAT6A/B inhibitor WM-1119

city: Parkville

first: Alexandra

last: Garnham

state: Victoria

address: 1G Royal Parade

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Acetylation of histones by lysine acetyltransferases (KATs) is essential for chromatin organization and function. The MYST family of KATs (KAT5-8) includes the oncogenes KAT6A (MOZ) and KAT6B (MORF/QKF). KAT6A has essential roles in normal hematopoietic stem cells and is the target of recurrent chromosomal translocations, causing acute myeloid leukemia. Similarly, chromosomal translocations in KAT6B have been identified in diverse cancers. KAT6A suppresses cellular senescence via regulation of suppressors of the CDKN2A locus, a function that requires its KAT activity. Loss of one allele of KAT6A extends the median survival of mice with MYC-induced lymphoma from 105 to 413 days. These findings suggest that inhibition of KAT6A and KAT6B may provide a therapeutic benefit in cancer. We have produced a series of highly potent, selective inhibitors of KAT6A/B including WM-8014 and WM-1119. Biochemical and structural studies demonstrate that these compounds are reversible acetyl-CoA competitors and inhibit MYST-catalyzed histone acetylation. WM-8014 and WM-1119 induce cell cycle exit and cellular senescence without causing DNA damage. Senescence is INK4A/ARF dependent and accompanied by gene expression changes typical of loss of KAT6A function. We anticipate that this class of inhibitors will be useful in accelerating development of therapeutics targeting gene transcription regulated by histone acetylation. We show that WM-1119 arrests lymphoma progression in mice. The B cell lymphoma cell line, EMRK1184, was isolated from Eμ-Myc transgenic mice, which are mice with a tumor resulting from the expression of cMyc under the control of the IgH enhancer. EMRK1184 expresses the Cdnk2a locus-encoded ARF and wild type p53. Treatment with WM-1119 inhibited the proliferation of the EMRK1184 lymphoma cells in vitro. RNA-seq and Western blot analysis showed that WM-1119 treatment resulted in increased levels of Cdkn2a and Cdkn2b mRNA and P16INK4a and p19ARF protein, as well as a delayed increase in Cdkn1a mRNA. The data here present RNA-seq profiling of EMRK1184 lymphomas treated with either WM-1119 or a control.

overall_design: EMRK1184 cells were infected with a luciferase-expressing lentiviral imaging construct to allow quantitation of tumor burden throughout treatment, producing the EMRK1184luc cell line. EMRK1184luc cells were treated with WM-1119 or a control and profiled by RNA-seq. Three biological replicates per treatment condition were prepared and sequenced. RNA-seq was undertaken for n=3 samples treated with DMSO for 3 days, n=3 samples treated with DMSO for 6 days, n=3 samples treated with WM-1119 for 3 days and n=3 samples treated with WM-1119 for 6 days.

first: Anne

last: Voss

first: Tim

last: Thomas

first: Gordon

last: Smyth


title: Inhibition of the MYST histone acetyltransferases KAT6A/B arrests lymphoma progression


title: RNA-seq profiling of mouse embryonic fibroblasts from Kat6a knockout and wildtype mice

summary: Acetylation of histones by lysine acetyltransferases (KATs) is essential for transcriptional regulation of gene expression. The MYST family of KATs (KAT5-8) includes the oncogenes KAT6A (MOZ) and KAT6B (MORF/QKF). KAT6A has key roles in promoting cell proliferation through transcriptional activation of negative regulators of the Cdkn2a locus, which encode the tumor suppressors INK4A and ARF. To examine the loss of KAT6A function, mouse embryonic fibroblasts (MEFs) were isolated from E13.5 Kat6a+/+ and Kat6a–/– embryos and RNA-seq profiling was performed.

overall_design: Two biological replicates of wildtype MEFs and three biological replicates of Kat6a knock-out MEFs were prepared.


title: Characterization of endothelial and smooth muscle cells from different canine vessels

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

summary: Canine primary endothelial cells (ECs) and vascular smooth muscle cells (vSMCs) were isolated from the vena cava, vena porta and aorta. All tissue sources were derived from three donors for accurate comparison and to reduce inter-animal variation. We used a recently established technique for the isolation of primary ECs with a lesser chance of contamination that can also be used on small vessels. This same vessel was also used for the isolation of vSMCs

overall_design: whole transriptome data of canine endothelial cells and vascular smooth muscle cells produced on Illumina NextSeq500 using a single-end 75 bp configuration

first: Loes

middle: A

last: Oosterhoff

first: Hedwig

last: Kruitwagen

first: Monique

last: van Wolferen

first: Bas

middle: W

last: van Balkom

first: Michal

last: Mokry

first: Nico

last: Lansu

first: Noortje

last: van den Dungen

first: Louis

last: Penning

first: Talitha

last: Spanjersberg

first: Johannes

last: de Graaf

first: Tomas

last: Veenendaal

first: Flin

last: Zomerdijk

first: Joost

middle: O

last: Fledderus

first: Bart

last: Spee

middle: G


title: Erythro-myeloid progenitors contribute endothelial cells to developing blood vessels

status: Public on Aug 02 2018

city: London

first: Alessandro

last: Fantin

state: - None -

address: 11-43 Bath Street

department: UCL Institute of Ophthalmology

institute: University College London

summary: The earliest blood vessels in the mammalian embryo are formed when endothelial cells (ECs) differentiate from angioblasts and coalesce into tubular networks. Thereafter, the en-dothelium is thought to expand solely by proliferation of pre-existing ECs. Here we show that the earliest precursors of erythrocytes, megakaryocytes and macrophages, the yolk sac-derived erythro-myeloid progenitors (EMPs), provide a complementary source of ECs that are recruited into pre-existing vasculature. Whereas a first wave of yolk sac-resident EMPs contributes ECs to the yolk sac endothelium, a second wave of EMPs colonises the embryo and contributes ECs to intraembryonic endothelium in multiple organs, where they persist into adulthood. By demonstrating that EMPs constitute a hitherto unrecognised source of ECs, we reveal that embryonic blood vascular endothelium expands in a dual mechanism that involves both the proliferation of pre-existing ECs and the incorporation of ECs derived from hematopoietic precursors.

overall_design: RNAseq analysis of FACS-isolated tdTom+ and tdTom- ECs from E12.5 Csf1r-iCre;RosatdTom embryos.

first: Alice

last: Plein

first: Christiana

last: Ruhrberg


title: Sequentially Acting SOX Proteins Orchestrate Astrocyte and Oligodendrocyte Specific Gene Expression

city: Stockholm

first: Jonas

last: Muhr

address: Biomedicum D5

department: CMB

country: Sweden

institute: Karolinska Institutet

summary: SOX transcription factors have important roles during astrocyte and oligodendrocyte development, but how glial genes are specified and activated in a sub-lineage specific fashion remains unknown. To address this question, we have defined glial specific gene expression in the developing spinal cord using single-cell RNA-sequencing. Moreover, conducting ChIP-seq analyses we show that these glial gene sets are extensively preselected already in multipotent neural precursor cells through the prebinding by SOX3. In the subsequent lineage-restricted glial precursor cells, astrocyte genes become additionally targeted by SOX9 at DNA-regions strongly enriched for Nfi binding-motifs, whereas oligodendrocyte genes become prebound by SOX9 only, at sites that during oligodendrocyte maturation are targeted by SOX10. Interestingly, reporter gene assays and functional studies in the spinal cord revealed that SOX3 binding represses the synergistic activation of astrocyte genes by SOX9 and NFIA, whereas oligodendrocyte genes are activated in a combinatorial manner by SOX9 and SOX10. These genome-wide studies demonstrate how sequentially expressed SOX proteins act on lineage-specific regulatory DNA-elements to coordinate glial gene expression both in a temporal and sub-lineage specific fashion.

overall_design: SOX3 ChIPseq (2 replicates), SOX9 ChIPseq (3 replicates), NFIA ChIPseq (2 replicates), Hsk27Ac ChIPseq (3 replicates), GPC RNAseq (4 replicates), Glial cells (3 replicates)

first: Maria

last: Bergsland

first: Zhanna

last: Alekseenko

first: Cécile

last: Zaouter


title: Group I Paks are essential for epithelial-mesenchymal transition in an Apc-driven mouse  model of colorectal cancer

city: Cincinnati

first: C.

middle: Alexander

last: Valencia

state: OH

address: 3333 Burnet Ave

department: Division of Human Genetics

institute: Cincinnati Children's Hospital Medical Center

summary: p21-activated kinases (Paks) play an important role in oncogenic signaling pathways, and have  therefore been considered as potential therapeutic targets in various cancers. Most studies of  Pak function employ loss of function methods such as gene knock-out or knock-down, but these  approaches result in loss of both the enzymatic and scaffolding properties of these proteins, and  thus may not reflect the effects of small molecule inhibitors that block catalytic function. In this  study we use a new transgenic mouse model in which a specific peptide inhibitor of Group I  Paks (Pak1, -2, and -3) is conditionally expressed in response to Cre recombinase. Using this  model, we show that inhibition of endogenous Pak function impedes the transition of adenoma  to carcinoma in an Apc-driven mouse model of colorectal cancer. These effects are mediated by  inhibition of Wnt signaling through reduced β-catenin activity as well as suppression of an  epithelial-mesenchymal transition program mediated by miR-200 and Snai1. These results  highlight the potential therapeutic role of Pak1 inhibitors in colorectal cancer and suggest new  therapeutic strategies in this disease.

overall_design: We generated a targeted transgenic mouse carrying a conditionally activated PID allele at the Rosa26 locus, and showed that expression of this allele effectively inhibited the activity of Group I Paks in vivo. To assess the global molecular effects of Pak inhibition in Apc-null CRC cells, we next explored the effect of repressing Pak activity on transcription. Total RNA was extracted from PID+ and PID- cells and RNA-sequencing was preformed, followed by pathway analysis and qPCR validation for selected mRNAs.

first: H

middle: Y

last: Chow

first: B

last: Don

first: C

first: J

last: Koch

last: Chernoff


title: RNA-seq profiling of mouse embyonic fibroblasts treated with the Myst inhibitor WM-8014

first: Alexandra

last: Garnham

summary: Acetylation of histones by lysine acetyltransferases (KATs) is essential for transcriptional regulation of gene expression. The MYST family of KATs (KAT5-8) includes the oncogenes KAT6A (MOZ) and KAT6B (MORF/QKF). KAT6A has key roles in promoting cell proliferation through transcriptional activation of negative regulators of the Cdkn2a locus, which encode the tumor suppressors INK4A and ARF. We produced a series of highly potent, selective inhibitors of KAT6A/B including WM-8014 and WM-1119. Biochemical and structural studies demonstrate that these compounds are reversible acetyl-CoA competitors. WM-8014 and WM-1119 inhibit MYST-catalyzed histone acetylation, thereby inducing cell cycle exit and cellular senescence, without causing DNA damage. The data here examine the transcriptional effects of WM-8014. Mouse embryonic fibroblasts (MEFs) were treated with either WM-8014 or with WM-2474, an inactive control, for either 96 hours or 240 hours and RNA-seq profiling was undertaken.

overall_design: Three biological replicates were prepared and sequenced. RNA-seq was undertaken for n=3 MEF samples treated with WM-2474 for 96 hours, n=3 MEF samples treated with WM-2474 for 240 hours, n=3 MEF samples treated with WM-8014 for 96 hours and n=3 MEF samples treated with WM-8014 for 240 hours.

first: Anne

last: Voss

first: Tim

last: Thomas

middle: L

first: Gordon

last: Smyth


title: Single-cell chromatin conformation capture of diploid cells by Dip-C (analyzed with the dip-c package)

status: Public on Aug 15 2018

city: Cambridge

first: Longzhi

last: Tan

address: 12 Oxford St

department: Chemistry and Chemical Biology

institute: Harvard University

type:
Other
Third-party reanalysis

summary: To reconstruct the 3D genomes of single diploid human and mouse cells, we performed single-cell chromatin conformation capture by a novel method, Dip-C, on human cells, and re-analyzed published data on mouse cells by the Dip-C algorithm.

sample_organism:
Homo sapiens
Mus musculus

overall_design: We performed Dip-C on 17 GM12878 human lymphoblastoid cells and 18 peripheral blood mononuclear cells (PBMCs) from a male human donor, and re-analyzed published data (GSE94489) on 10 mouse embryonic stem cells (mESCs) from a hybrid mouse. For 3D reconstruction, we performed 3 replicates per human cell and 5 replicates per mouse cell. BioProject for the human data is PRJNA473369.


title: Heat shock-induced ribosomal intergenic spacer RNA

city: Miami

first: Stephen

last: Lee

state: Florida

department: Biochemistry & Molecular Biology

institute: University of Miami

summary: Cells adapt to environmental stressors such as heat shock and extracellular acidosis through formation of nuclear membrane-less compartments called Amyloid bodies (A-bodies). Stressors activate formation of Amyloid bodies (A-bodies) via induction of ribosomal intergenic spacer RNA (rIGSRNA). RNA-seq on non-ribosome depleted RNA from human MCF7 cells exposed to heat shock (43C, 30 minutes) revealed the heat shock-specific expression profile of rIGSRNA.

overall_design: Expression profile of the ribosomal intergenic spacer (i.e. rIGSRNA) in cells exposed to heat shock

first: Miling

last: Wang


title: RNA-seq profiling of mouse embryonic fibroblasts treated with WM-2474 or DMSO

summary: Acetylation of histones by lysine acetyltransferases (KATs) is essential for chromatin organization and function. The MYST family of KATs (KAT5-8) includes the oncogenes KAT6A (MOZ) and KAT6B (MORF/QKF). KAT6A has essential roles in normal hematopoietic stem cells and is the target of recurrent chromosomal translocations, causing acute myeloid leukemia. Similarly, chromosomal translocations in KAT6B have been identified in diverse cancers. KAT6A suppresses cellular senescence via regulation of suppressors of the CDKN2A locus, a function that requires its KAT activity. Loss of one allele of KAT6A extends the median survival of mice with MYC-induced lymphoma from 105 to 413 days. These findings suggest that inhibition of KAT6A and KAT6B may provide a therapeutic benefit in cancer. We have produced a series of highly potent, selective inhibitors of KAT6A/B including WM-8014 and WM-1119, which we anticipate will be useul in accelerating development of therapeutics. For comparison purposes, we also generated an inactive analogue WM-2474 as a control treatment. The data here focus on WM-2474 and present RNA-seq profiling of mouse embryonic fibroblasts (MEFs) treated with either WM-2472 or DMSO.

overall_design: Three biological replicates per treatment condition were prepared and sequenced. RNA-seq was undertaken for n=3 MEF samples treated with DMSO for 96 hours, n=3 MEF samples treated with DMSO for 240 hours, n=3 MEF samples treated with WM-2474 for 96 hours and n=3 MEF samlpes treated with WM-2474 for 240 hours.


title: RNA-sequencing of Adult Mouse Inner Hair Cells and Outer Hair Cells of the organ of Corti

first: David

last: He

summary: To further understand the biological properties of hair cells of the mammalian cochlea, we examined the transcriptome of adult inner and outer hair cells. Morphologically distinct inner and outer hair cells were isolated from the organ of Corti from adult CBA/J mice. One thousand inner and outer hair cells were separately collected for each biological replicate, using the suction pipette technique. RNA sequencing of two biological replicates of IHCs and three biological replicates of OHCs, each with two technical repeats, was performed. The resulting sequenced reads were mapped. Comparisons between inner and outer hair cells allow identification of enriched genes, as well as differentially expressed genes that result in cellular specialization. Our dataset provides an extensive resource for understanding the molecular mechanisms underlying morphology, function, and pathology of adult mouse inner and outer hair cells.

overall_design: One thousand inner hair cells and 1,000 outer hair cells were separately collected for each biological replicate, using the suction pipette technique. RNA sequencing of two or three biological replicates, for inner hair cells and outer hair cells respectively, was performed. The resulting sequenced reads were mapped. Comparisons between inner and outer hair cells allow identification of enriched genes which may underlie cell specialization.

first: Huizhan

last: Liu

first: Lei

last: Chen

first: Kimberlee

middle: P

last: Giffen

first: Sean

last: Stringham

first: Yi

last: Li

first: Paul

last: Judge

first: Kirk

last: Beisel


title: Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis. [RNA-seq]

city: Boston

first: Cigall

last: Kadoch

address: 450 Brookline Avenue

department: Pediatric Oncology

institute: Dana-Farber Cancer Institute

summary: Chromosomal rearrangements resulting in the fusion of TMRPSS2, an androgen-regulated gene, and the ETS family transcription factor ERG occur in over half of prostate cancers. However, the mechanism by which ERG promotes oncogenic gene expression and proliferation remains incompletely understood. Here, we identify a binding interaction between ERG and the mammalian SWI/SNF (BAF) ATP-dependent chromatin remodeling complex, which is conserved among other ETS factors, including ETV1, ETV4, and ETV5. We find that ERG drives genome-wide retargeting of BAF complexes in a manner dependent on binding of ERG to the ETS DNA motif. Moreover, ERG requires intact BAF complexes for chromatin occupancy and BAF complex ATPase activity for target gene regulation.  In a prostate organoid model, BAF complexes are required for ERG-mediated basal-to-luminal transition, a hallmark of ERG activity in prostate cancer. These observations suggest a fundamental interdependence between ETS transcription factors and BAF chromatin remodeling complexes in cancer.

overall_design: Prostate cancer cell lines (VCaP, LNCaP) and adrenacorticoid carcinoma cell lines (SW13) were lentivirally infected with respective expression/knockdown constructs, selected, and harvested for RNA-seq.

first: John

last: Pulice


title: Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis.

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

overall_design: Refer to individual Series


title: The microRNA miR-21 is a mediator of FGF8 action on cortical COUP-TFI translation

status: Public on Aug 01 2018

city: Pisa

first: Marco

last: Terrigno

address: Via Giuseppe Moruzzi, 1

country: Italy

institute: Scuola Normale Superiore

summary: These data support a translational control of COUP-TFI gradient expression by FGF8 via miR-21 and contribute to our understanding of how regionalized expression is established during neocortical area mapping

overall_design: 8 samples in 4 groups: Control 24 h (2 samples), FGF8 24 h (2 samples), control 48 h (2 samples), FGF8 48 h (2 samples)

first: Michele

last: Bertacchi

first: Luca

last: Pandolfini

first: Mario

last: Baumgart

first: Mariantonietta

last: Calvello

first: Alessandro

last: Cellerino

first: Michèle

last: Studer

first: Federico

last: Cremisi

last: Groth


title: SNON and Arkadia (RNF111) regulate TGFβ-SMAD2/3 dose-dependent responses

first: Vasso

last: Episkopou

address: Du Cane Road

department: Brain Sciences

institute: Imperial College London

summary: The purpose of this RNA-seq experiment was to identify Activin A target genes that were differentially expressed in wild type and Arkadia null mouse embryonic stem cells (ESC). We performed the RNA sequencing experiment in two different wt and Arkadia-/- ESC under conditions of signalling inhibition SB431542 (SB; T0) and signalling stimulation with Activin A for 3 and 6 hours (T3 and T6 respectively).

overall_design: RNA-sequencing performed on two wt and two Arkadia -/- mouse embryonic stem cell lines treated with receptor kinase inhibitor (SB431542) or Activin A for 3 and 6 hours.

first: Jonathon

last: Carthy


title: Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis.[ChIP-seq]

overall_design: Prostate cancer cell lines (VCaP, LNCaP) were lentivirally infected with respective expression/knockdown constructs, selected, and harvested for ChIP-seq.


title: Influenced genes by miR663a

city: BEIJING

first: WEI

last: TIAN

address: FUCHENG ROAD 52#

institute: BEIJING CANCER HOSPITAL

summary:
An increasing number of studies have demonstrated that miRNAs may act as oncogenes or anti-oncogenes in various types of cancer, including colon carcinoma (CC). However the clinical and biological signiﬁcance of miR663a in the prognosis of CC and its underlying mechanisms remain unknown.
In our study, it was found that miR663a was significantly downregulated in CC, especially in metastatic CC tissues. MiR663a overexpression not only inhibited the proliferation and migration/invasion of CC cells in vitro, but also inhibited tumor growth and metastasis of CC cells in vivo. However the mechanism under that was still unknown. So miR663a target genes were  analyzed in our project.

overall_design: To explore the target genes of miR663a which mediated its function, we overexpressed miR663a and its inhibitor in HCT116 cells and did the cDNA array to screen out the genes whose expression level was inhibited by miR663a overexpression and promoted by miR663a inhibition.

first: Yantao

last: Du

first: Wei

last: Tian


title: Comparative bulk RNAseq analysis of Control and PTH/PTHrP recepter-deficient PTHrP+ dental follicle cells

city: Houston

first: Noriaki

last: Ono

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

summary: Lack of PTH/PTHrP receptor in PTHrP+ dental follicle cells causes a cell fate shift and premature differentiation. Here, we set out to reveal the transcriptome change induced by deficiency in PTH/PTHrP receptor in PTHrP+ dental follicle cells

overall_design: tdTomato+ cells were FACS-isolated from postnatal day 8 (P8) dental follicles of Pth1r conditional Het and conditional KO mandibular molars (tamoxifen pulse at P3). mRNA were amplifed by SMARTer mRNA-seq kit (Clonetech/Takara) before deep-sequenced by Illumina HiSeq4000.


title: Functional characteristics of novel pancreatic Pax6 regulatory using a mouse pancreatic cell model

city: Edinburgh

first: nick

last: gilbert

address: Crewe Rd

department: MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

summary: Transcriptome profiling using RNA-seq of β-TC3 cell, a mouse pancreatic cell line used in the study of novel Cis-regulatory elements for the Pax6 gene .

overall_design: Total RNA was collected and a Illumina sequencing libraries prepared from two biological replicates of cultured β-TC3 cells.

first: Adam

last: Buckle

first: Ryu-Suke

last: Nozawa

first: Dirk

last: Kleinjan

first: Nick

last: Gilbert


title: RNA-seq of P14 mouse brain, WT and PRMT5 olig2-cre KO

city: Montreal

first: Stéphane

last: Richard

state: Quebec

address: 3755 Chemin de la Côte-Sainte-Catherine

institute: Lady Davis Institute for Medical Research - Jewish General Hospital, McGill University

summary: Analysis of the transcriptiome of p14 mouse brains to investigate the contribution of PRMT5 in oligodendrocyte gene expression and alternative splicing regulation

overall_design: P14 mouse brain were analyzed in triplicates by Illumina RNA-seq

first: Sara

last: Calabretta

first: Karine

last: Choquet


title: E-cadherin bridges cell polarity and spindle orientation to ensure prostate epithelial integrity and prevent carcinogenesis in vivo

city: Shanghai

first: Xue

last: Wang

state: Shanghai China

address: Huashan Rd. 1940, build 3.  Shanghai,

institute: SJTU CHINA

summary: Cell polarity and correct mitotic spindle positioning are essential for the maintenance of a proper prostate epithelial architecture, and disruption of the two biological features occurs at early stages in prostate tumorigenesis. However, whether and how these two epithelial attributes are connected in vivo is largely unknown. We herein report that conditional genetic deletion of E-cadherin, a key component of adherens junctions, in a mouse model results in loss of prostate luminal cell polarity and randomization of spindle orientations. Critically, E-cadherin ablation causes prostatic hyperplasia which progresses to invasive adenocarcinoma. Mechanistically, E-cadherin and the spindle positioning determinant LGN interacts with the PDZ domain of cell polarity protein SCRIB and form a ternary protein complex to bridge cell polarity and cell division orientation. These findings provide a novel mechanism by which E-cadherin acts an anchor to maintain prostate epithelial integrity and to prevent carcinogenesis in vivo.

overall_design: Exploration of the transcriptional difference between E-cadherin conditional knockout  mice and their control littermates

first: Helen

middle: H

last: Zhu


title: Nuclear actin is required for transcription during Drosophila oogenesis [RNA-seq]

city: Helsinki

first: Maria

last: Sokolova

address: Viikinkaari 5

department: Institute of Biotechnology

country: Finland

institute: University of Helsinki

summary: we performed transcriptomic analysis of the RanBP9del1   mutant ovaries compared to wild type

overall_design: explore the consequences of decreased nuclear actin on transcription


title: Accurate classification of BRCA1 variants with saturation genome editing

city: Seattle

first: Lea

middle: M

last: Starita

state: WA

department: Genome Sciences

institute: University of Washington

summary: We describe the use of saturation genome editing to make and measure the effect of BRCA1 variants on protein function and splicing. We find the results accurately predict the clinical effects of variants.

overall_design: Saturation genome editing of the BRCA1 exons encoding the RING and BRCT domain.

first: Gregory

last: Findlay

first: Riza

last: Daza

first: Beth

last: Martin

first: Melissa

last: Zhang

first: Anh

last: Leith

first: Molly

last: Gasperini

first: Joseph

last: Janizek

first: Xingfan

last: Huang

first: Jay

last: Shendure


title: A Single-Cell Atlas of In Vivo Mammalian Chromatin Accessibility

city: Tucson

first: Darren

middle: A.

last: Cusanovich

state: AZ

address: 1230 N Cherry Avenue, BSRL 421

department: Cellular and Molecular Medicine

institute: University of Arizona

summary: We applied a combinatorial indexing assay, sci-ATAC-seq, to profile genome-wide chromatin accessibility in ~100,000 single cells from 13 adult mouse tissues. We identify 85 distinct patterns of chromatin accessibility, most of which can be assigned to cell types, and ~400,000 differentially accessible elements. We use these data to link regulatory elements to their target genes, to define the transcription factor grammar specifying each cell type, and to discover in vivo correlates of heterogeneity in accessibility within cell types. We develop a technique for mapping single cell gene expression data to single-cell chromatin accessibility data, facilitating the comparison of atlases. By intersecting mouse chromatin accessibility with human genome-wide association summary statistics, we identify cell-type-specific enrichments of the heritability signal for hundreds of complex traits. These data define the in vivo landscape of the regulatory genome for common mammalian cell types at single-cell resolution.

overall_design: sci-ATAC-seq data was collected on 13 different tissues (replicates were collected for 4 tissues) from 8-week-old male C57BL/6J mice. In total, we collected data on just over 100,000 individual cells, which were filtered down to 81,173 cells after quality control. Custom scripts for processing data are available at atlas.gs.washington.edu.

first: Andrew

middle: J

last: Hill

first: Delasa

last: Aghamirzaie

first: Hannah

last: Pliner

first: Joel

middle: B

last: Berletch

first: Galina

middle: N

last: Filippova

first: Lena

last: Christiansen

first: William

last: DeWitt

first: Choli

last: Lee

first: Samuel

last: Regalado

first: David

middle: F

last: Read

first: Frank

last: Steemers

first: Christine

last: Disteche

first: Cole

last: Trapnell


title: Effect of CRISPR-Cas9 mediated knock-out of integrin alpha2 on the transcriptome of DU145 prostate cancer cell grown as a spheroid culture

city: Turku

first: Jyrki

last: Heino

address: Vatselankatu 2

department: Biochemistry

institute: University of Turku

summary: CRISPR-cas9 technology was used to knock out alpha2 integrin in DU145 cells. To create two cell lines that could be compared to each other in an appropriate manner, these cells were transfected either with alpha2 integrin cDNA or empty vector. The objective of the study was to find potential alpha2 integrin regulated genes when the cells were grown as spheroids.

overall_design: The DU145 with a2 integrin knockout, the knockouts transfected by a2 integrin expressing vector or empty vector were analyzed. Each of the three groups contained four biological replicates.

first: Marjaana

last: Ojalill

first: Pekka

last: Rappu

first: Johanna

last: Jokinen


title: Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data

address: 3720 15th Ave NE

summary: Linking regulatory DNA elements to their target genes, which may be located hundreds of kilobases away, remains challenging. Here, we introduce Cicero, an algorithm that identifies co-accessible pairs of DNA elements using single-cell chromatin accessibility data and so connects regulatory elements to their putative target genes. We apply Cicero to investigate how dynamically accessible elements orchestrate gene regulation in differentiating myoblasts. Groups of Cicero-linked regulatory elements meet criteria of “chromatin hubs”—they are enriched for physical proximity, interact with a common set of transcription factors, and undergo coordinated changes in histone marks that are predictive of changes in gene expression. Pseudotemporal analysis revealed that most DNA elements remain in chromatin hubs throughout differentiation. A subset of elements bound by MYOD1 in myoblasts exhibit early opening in a PBX1- and MEIS1-dependent manner. Our strategy can be applied to dissect the architecture, sequence determinants, and mechanisms of cis-regulation on a genome-wide scale.

overall_design: sci-ATAC-seq data was collected on human skeletal muscle myoblasts (HSMM) in culture at four timepoints after serum switch to induce differentiation into myotubes, 0 hours, 24 hours, 48 hours and 72 hours. Libraries pooled for sequencing (Experiment 1). An additional experiment was collected using the same system, at 0 hours and 72 hours after serum switch (Experiment 2). Bulk ATAC-seq data was also collected for each of the four timepoints. In addition, sci-ATAC-seq data was collected on an artificial mixture of GM12878 and HL60 cells. Lastly, bulk ATAC-seq data was collected at day 0 and day 7 after serum switch in 54-1 immortalized myoblasts that were transduced with lentivirus carrying small guide RNAs targeting Pbx1, Meis1 or non-targeting controls using lentiCRISPRv2-blast. Cells were allowed time for editing post transduction before differentiation.  See publication for details.

first: Jonathan

last: Packer

first: José

last: McFaline-Figueroa

first: Darren

last: Cusanovich

first: Riza

last: Daza

first: Sanjay

last: Srivatsan

first: Xiaojie

last: Qiu

first: Dana

last: Jackson

first: Anna

last: Minkina

first: Andrew

last: Adey

first: Jay

last: Shendure


title: Co-regulation of alternative splicing by hnRNPM and ESRP1 during EMT

first: Samuel

middle: Emerson

last: Harvey

state: TEXAS

address: One Baylor Plaza

department: Lester and Sue Smith Breast Center

institute: Baylor College of Medicine

summary: The epithelial-mesenchymal transition (EMT) is a fundamental developmental process that is abnormally activated in cancer metastasis. Dynamic changes in alternative splicing occur during EMT. ESRP1 and hnRNPM are splicing regulators that promote an epithelial splicing program and a mesenchymal splicing program, respectively. The functional relationships between these splicing factors in the genome-scale remain elusive. Comparing alternative splicing targets of hnRNPM and ESRP1 revealed that they co-regulate a set of cassette exon events, with the majority showing discordant splicing regulation. hnRNPM discordantly regulated splicing events show a positive correlation with splicing during EMT while concordant splicing events do not, highlighting the antagonistic role of hnRNPM and ESRP1 during EMT. Motif enrichment analysis near co-regulated exons identifies guanine-uridine rich motifs downstream of hnRNPM-repressed and ESRP1-enhanced exons, supporting a model of competitive binding to these cis-elements to antagonize alternative splicing. The set of co-regulated exons are enriched in genes associated with cell-migration and cytoskeletal reorganization, which are pathways associated with EMT. Splicing levels of co-regulated exons are associated with breast cancer patient survival and correlate with gene sets involved in EMT and breast cancer subtypes. In conclusion, hnRNPM and ESRP1 co-regulate antagonistically a set of alternative splicing events that occur during EMT. This regulation is likely mediated through competition for the same intronic binding sites downstream of variable exons. hnRNPM and ESRP1 regulated splicing events are associated with breast cancer survival.

overall_design: PolyA-RNA-sequencing of control and hnRNPM knockdown cell lines

first: Chonghui

last: Cheng

middle: E


title: Genetic and transcriptional variation alters cancer cell line drug response [MCF7 strain AA]

first: Yaara

last: Oren

state: Massachusetts

address: 415 MAIN

department: Cell circuits

institute: Broad

summary:
10X Genomics single cell RNAseq of MCF7 cells treated with bortezomib.
Human cancer cell lines are the workhorse of cancer research. While cell lines are known to evolve in culture, the extent of the resultant genetic and transcriptional heterogeneity and its functional consequences remain understudied. Here, genomic analyses of 106 cell lines grown in two laboratories revealed extensive clonal diversity. Follow-up comprehensive genomic characterization of 27 strains of the common breast cancer cell line MCF7 uncovered rapid genetic diversification. Similar results were obtained with multiple strains of 13 additional cell lines. Importantly, genetic changes were associated with differential activation of gene expression programs and marked differences in cell morphology and proliferation. Barcoding experiments showed that cell line evolution occurs as a result of positive clonal selection that is highly sensitive to culture conditions. Analyses of single cell-derived clones showed that ongoing instability quickly translates into cell line heterogeneity. Testing of the 27 MCF7 strains against 321 anti-cancer compounds uncovered strikingly disparate drug response: at least 75% of compounds that strongly inhibited some strains were completely inactive in others. This study documents the extent, origin and consequence of genetic variation within cell lines, and provides a framework for researchers to measure such variation in efforts to support maximally reproducible cancer research.

overall_design: MCF7 cells (strain AA) were treated with bortezomib (500nM) and harvested before treatment, after 12 hours of exposure (t12), after 24 hours of exposure (t48), or after 72 hours of exposure followed by drug wash and 24 hours of recovery (t72+24)

first: Uri

last: Ben-David


title: Targeting tumour re-wiring by triple blockade of mTORC1, epidermal growth factor and estrogen receptor signalling pathways in endocrine resistant breast cancer

first: Eugene

last: Schuster

address: 123 Old Brompton Road

department: Breast Cancer Research

institute: Institute of Cancer Research

summary: Our data supports the potential combination of inhibition of ERBB2/3 signalling with mTORC1 perturbation and endocrine therapy in patients who have relapsed on endocrine therapy and retain a functional ER.

overall_design: RNAseq examination of gene expression changes in MCF72a-LTED tumour xenografts due to treatment with RAD001 (RAD), the pan-ERBB inhibitor neratinib (Ner) and fulvestrant ICI182780 (Ful)

first: Lesley-Ann

last: Martin


title: Genetic and transcriptional variation alters cancer cell line drug response [MCF7]

summary:
10X Genomics single cell RNAseq of MCF7 cells
Human cancer cell lines are the workhorse of cancer research. While cell lines are known to evolve in culture, the extent of the resultant genetic and transcriptional heterogeneity and its functional consequences remain understudied. Here, genomic analyses of 106 cell lines grown in two laboratories revealed extensive clonal diversity. Follow-up comprehensive genomic characterization of 27 strains of the common breast cancer cell line MCF7 uncovered rapid genetic diversification. Similar results were obtained with multiple strains of 13 additional cell lines. Importantly, genetic changes were associated with differential activation of gene expression programs and marked differences in cell morphology and proliferation. Barcoding experiments showed that cell line evolution occurs as a result of positive clonal selection that is highly sensitive to culture conditions. Analyses of single cell-derived clones showed that ongoing instability quickly translates into cell line heterogeneity. Testing of the 27 MCF7 strains against 321 anti-cancer compounds uncovered strikingly disparate drug response: at least 75% of compounds that strongly inhibited some strains were completely inactive in others. This study documents the extent, origin and consequence of genetic variation within cell lines, and provides a framework for researchers to measure such variation in efforts to support maximally reproducible cancer research.

overall_design: Single cell clones were derived from MCF7 cells and cultured.


title: Impact of chorioamnionitis exposure on neonatal monocyte H3K4me3 patterning

city: Iowa City

first: Jennifer

middle: Rachelle

last: Bermick

state: IA

address: 431 Newton Road, 505 EMRB

department: Pediatrics

institute: University of Iowa

summary: We sought to determine the impact of chorioamnionitis exposure on the neonatal monocyte H3K4me3 histone modification landscape over the course of fetal and neonatal immune system development using ChIP-seq.  H3K4me3 ChIP-seq was performed on umbilical cord blood purified CD14+ monocytes from healthy and chorioamnionitis-exposed extremely preterm neonates (under 30 weeks gestation), late preterm neonates (30-36 weeks gestation), and term neonates (37+ weeks gestation).

overall_design: H3K4me3 ChIP-seq on 9 samples with 3 replicates per age group (each replicate contains 3 pooled samples)

middle: R


title: Effect of chorioamnionitis exposure on neonatal monocyte transcription

summary: We sought to determine the impact of chorioamnionitis exposure on term neonatal monocyte transcription. RNA-seq was performed on term healthy and chorioamnionitis-exposed umbilical cord blood purified CD14+ monocytes under unstimulated and LPS stimulated conditions.

overall_design: RNA-seq on 11 samples with 2-3 replicates per exposure/stimulation group (each replicate contains 3 pooled samples)


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and L3mbtl2 cKO Testicular Transcriptomes

city: Hong Kong

first: Yin

last: Xia

address: LKIBSB

institute: The Chinese University of Hong Kong

summary: Our study represents the first detailed analysis of testicular transcriptomes, with biologic replicates, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles.

overall_design: Testicular mRNA profiles of 8-month-old contol and L3mbtl2 cKO mice were generated by deep sequencing, in triplicate, using Illumina HiSeq platform.

first: Chenling

last: Meng


title: Genetic and transcriptional variation alters cancer cell line drug response

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

overall_design: Refer to individual Series


title: Angiotensin Converting Enzyme Inhibition Attenuates Interstitial Injury in a Murine Model of Chronic Glomerulonephritis

city: Syracuse

first: Frank

middle: A

last: Middleton

state: NY

address: 505 Irving Avenue

department: Neuroscience and Physiology

institute: SUNY Upstate Medical Univ

summary: This study examined the role of local complement synthesis in a mouse model of glomerulonephritis, which evolves into progressive tubulointerstitial disease.  The model was used to quantitate clinical, histologic, and transcriptomic outcomes, and assess the role of angiotensin conversting enzyme (ACE) inhibition in modifying these measures.  We also comprehensively explored the biological pathways and networks exhibiting alterations in gene expression to provide further insight into the role of ACE inhibition in the model.

overall_design: C57BL/6 mice were purchased from The Jackson Laboratories (Bar Harbor, ME).  Glomerulonephritis (GN) was induced by the intraperitoneal (IP) injection of 10 mg horse spleen apoferritin (HSA; Sigma, St. Louis, MO) five times weekly for six weeks.  Lipopolysaccharide (LPS from Salmonella Minnesota; EMD Biosciences, La Jolla, CA) at a dose of 100 micrograms was also given IP three times weekly as adjuvant, also for six weeks.  Control mice received equivalent volumes of normal saline IP on the same schedule. At 9 weeks, mice were euthanized by CO2 inhalation and small sections of kidney cortex (20-30 mg) processed for RNA-sequencing.


title: Small sized mesenchymal stem-cells primed with hypoxia attenuate graft-versus-host disease

city: Seoul

first: DONG-MYUNG

last: SHIN

address: Pungnap-2 dong, Songpa-gu

department: Department of Biomedical Sciences

institute: University of Ulsan College of Medicine

type: Methylation profiling by genome tiling array


title: Small sized mesenchymal stem-cells primed with hypoxia attenuate graft-versus-host disease [transcriptome dataset]

summary: Mesenchymal stem-cells (MSCs) are of particular interest for treating immune-related diseases due to their immunosuppressive capacities. Here, we show that Small sized MSCs primed with Hypoxia and Calcium ion (SHC-MSCs) exhibit the enhanced functions regarding stemness and immunomodulation for treating allogeneic conflicts. Compared with naïve cultured human umbilical cord-blood MSCs, SHC-MSCs were resistant to the passage dependent cellular senescence mediated by MCP-1 and p53/p21 cascade and highly secreted the pro-angiogenic and immune-modulatory factors, resulting in suppression of T-cell proliferation. Genome-wide DNA methylome and transcriptome analysis indicate that SHC-MSCs characteristically up-regulated immune-modulation, cell adhesion and cell-cycle related genes. As downstream factors, PLK1, ZNF143, DHRS3, and FOG2 proteins played a key role on the beneficial effects of SHC-MSCs, evidenced by the promoted self-renewal, migration, pro-angiogenic, anti-inflammatory, and T cell suppression capacities in their-over-expressing MSCs. Importantly, administration of SHC-MSCs or PLK1-over-expressing cells (PLK1-MSCs) significantly reduced the symptoms of graft-versus-host disease (GVHD) in a humanized mouse model which led to significantly improved survival, less weight loss, and less histopathologic injuries of GVHD target organs compared with naive MSC-infused mice. Collectively, our study suggests that small-sized MSCs primed with hypoxia could advance the therapeutic strategy for the clinical treatment of allogeneic conflicts including GVHD.

overall_design: Human umbilical cord blood derived mesenchymal stem cells (UCB-MSCs) were normally maintained (NT) or cultivated by SHC procedure (SHC) which enriched small sized cells and at the same time primed with hypoxia ( 3 % oxygen) and calcium ion (1.8 mM). Total RNA from three independent replicates was isolated using the RNeasy Mini Kit (QIAGEN, Valencia, CA), including treatment with DNase I (QIAGEN). One ug of total RNA was used for the Affymetrix GeneChip Human 2.0 ST Array (Affymetrix, Santa Clara, CA), in accordance with the manufacturer’s instructions.

first: Dong-Myung

last: Shin

first: YongHwan

last: Kim

first: Hyein

last: Ju


title: Gene expression changes associated with Alexander disease (AxD)

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

summary: We use human induced pluripotent stem cell (hiPSC)-derived astrocytes and post-mortem human brain tissues to study gene expression changes associated with AxD

overall_design: To compare gene expression profiles in healthy control and AxD patient iPSC-derived astrocytes and post-mortem brain tissues

first: Shi

last: Yanhong

first: Li

last: Li


title: Single cell sequencing of BMP4 stimulated enteroendocrine cells in organoids

city: Utrecht

first: Joep

last: Beumer

address: Uppsalaan 8

institute: Hubrecht Institute

summary: Enteroendocrine cells (EECs) alter hormone expression while migrating along the crypt-villus axis. We report this swich is regulated by a BMP morphogen gradient. Single cell RNA sequencing of control and BMP4 stimulated EECs was performed using organoids from different hormone reporter mice. We show that BMP4 stimulation can switch different subsets of EECs from their crypt to villus state.

overall_design: We generated transciptome data from cells sorted from different hormone reporter mouse organoid lines with and without BMP4 stimulation, at different timepoints

first: Benedetta

last: Artegiani

first: Yorick

last: Post

last: Reimann

first: Fiona

last: Gribble

first: Thuc

last: Nghi Nguyen

first: Hongkui

last: Zeng

first: Maaike

last: Van den Born

first: Johan

last: Van Es

first: Hans

last: Clevers


title: Human cytotrophoblast organoids

city: Vienna

first: Paulina

middle: Anna

last: Latos

address: Schwarzspanierstraße 17

department: Center for Anatomy and Cell Biology

country: Austria

institute: Medical University of Vienna

summary: Human cytotrophoblast organoid cultures were established from the villous trophoblast of first trimester placentas. We analyzed the global expression profile of the cytotrophoblast organoids (CTB-ORG) and compared to the profile of the tissue of origin i.e. villous cytotrophoblast (vCTB) as well as to differentiated syncytiotrophoblast (STB) and placental fibroblasts (FIB).

overall_design: We employed QuantSeq method to analyzed the global expression profile of the cytotrophoblast organoids (4 replicates, CTB-ORG 1-4) and compared to the profile of the tissue of origin i.e. villous cytotrophoblast (3 replicates, vCTB 1-3) as well as to in vitro differentiated syncytiotrophoblast (3 replicates, STB1-3) and placental fibroblasts (2 replicates, FIB 1-2).

first: Sandra

last: Haider

first: Magdalena

last: Gamperl

first: Martin

last: Knoefler

first: Sasha

last: Mendjan

first: Thomas

last: Burkard


title: Genetic and transcriptional variation alters cancer cell line drug response [MCF7 strain L]

city: Cambridge

first: Yaara

last: Oren

overall_design: Single cell clones were derived from MCF7 cells (strain L) and cultured.

first: Uri

last: Ben-David