title: A single-cell RNA-Seq of human hepatocyte-derived liver progenitor-like cells

status: Public on Jun 22 2018

city: shanghai

first: yan

last: hexin

address: No. 1630 East Road

institute: Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine

summary: 10X Genomics Single Cell Gene Expression was performed to comprehensively characterize cell subpopulations within human hepatocyte-derived liver progenitor-like cells (HepLPCs).

overall_design: Human primary hepatocytes could convert into expandable liver progenitor-like cells in vitro within the transition and expansion medium. Human hepatocyte-derived liver progenitor-like cells (HepLPCs) were derived from one donor and cultured in the transition and expansion medium for passage 5.

first: Yan

middle: H

last: Xin

first: Fu

middle: G

last: Bo


title: RNA-sequencing (RNA-seq) of induced pluripotent stem cells (iPSC) and iPSC-derived astrocytes from control and Parkinson's disease patients carrying LRRK2 G2019S point mutation

city: Hospitalet de Llobregat (Barcelona)

first: Meritxell

last: Pons

address: Avinguda Gran Via, 199-203

country: Spain

institute: IDIBELL

type: Expression profiling by high throughput sequencing

summary:
Purpose: The goal of this study is to compare the NGS-derived from transcriptome profiling (RNA-seq) of human iPSC, human iPSC-derived astrocytes from control and Parkinson’s disease LRRK2 G2019S, and human commercial astrocytes to gain insight into the identity of human iPSC-derived astrocytes in vitro during the differentiation process.

Total RNA was assayed for quantity and quality using Qubit® RNA HS Assay (Life Technologies) and RNA 6000 Nano Assay on a Bioanalyzer 2100.  The RNASeq libraries were prepared from total RNA using the TruSeq®Stranded mRNA LT Sample Prep Kit (Illumina Inc., Rev.E, October 2013). Briefly, 500ng of total RNA was used as the input material and was enriched for the mRNA fraction using oligo-dT magnetic beads. The mRNA was fragmented in the presence of divalent metal cations and at high temperature (resulting RNA fragment size was 80-250nt, with the major peak at 130nt). The second strand cDNA synthesis was performed in the presence of dUTP instead of dTTP, this allowed to achieve the strand specificity. The blunt-ended double stranded cDNA was 3´adenylated and Illumina indexed adapters were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay.  The libraries were sequenced on HiSeq2000 (Illumina, Inc) in paired-end mode with a read length of 2x76bp using TruSeq SBS Kit v4. We generated over 30 million paired-end reads for each sample in a fraction of a sequencing v4 flow cell lane, following the manufacturer’s protocol. Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.18.66.3) and followed by generation of fastq.gz sequence files by CASAVA.

Results: We found that transcriptome of human iPSC-derived astrocytes is similar to human commercial astrocytes than human iPSC.

Conclusion: These results suggest that iPSC-derived astrocytes resemble human commercial astrocytes validating the differentiating protocol used.

overall_design: Human iPSC-derived astrocyte identity was obtained by comparing human iPSC from the same control and Parkinson’s disease LRRK2 G2019S patients and human commercial astrocytes. mRNA profiles were generated by deep sequencing using Illumina HiSeq2000.


title: T cell landscape of non-small cell lung cancer revealed by deep single-cell RNA sequencing

status: Public on Jun 25 2018

city: Beijing

first: zemin

last: zhang

address: Yiheyuan Road

department: BIOPIC

country: China

institute: Peking University

summary: Cancer immunotherapies have shown sustained clinical responses in treating non-small cell lung cancer (NSCLC), but the clinical outcome is not uniform among patients, with complex tumour-immune interactions playing key roles. To depict and dissect the baseline landscape of the composition, lineage and functional states of tumor-infiltrating lymphocytes (TILs) in lung cancer, here we generated deep single-cell RNA sequencing data for 12346 T cells from the tumour, adjacent normal tissues and peripheral blood from 14 treatment-naïve NSCLC patients. Based on expression and TCR-based lineage tracking, we found a significant proportion of effector memory T cells with the same origin and similar functional states across peripheral blood and tumours, indicating the existence of systemic T cell immunity. We also observed tumour-infiltrating CD8+ T cells undergoing extensive clonal expansion and exhaustion in tumours, with two clusters of cells exhibiting states preceding exhaustion. Survival analysis on independent datasets suggested that high ratio of “pre-exhausted” to exhausted T cells was associated with better prognosis of lung adenocarcinoma. In addition, we observed a specific cluster of tumour-specific regulatory T cells (Tregs), characterized by a set of immunosuppressive genes, and high expression of their signature genes, including IL1R2, correlated with poor prognosis of lung adenocarcinoma. These findings and the accompanying compendium of single cell data will help the research community to gain further insight into the functional states and dynamics of T cell responses in lung cancer.

overall_design: T cells from NSCLC patients were sorted, profiled by Smart-seq2 and sequenced on Illumina HiSeq2500/HiSeq4000. Based on FACS analysis, single cells of different subtypes, including CD8+ T cells (CD3+ and CD8+), T helper cells (CD3+, CD4+ and CD25-), and regulatory T cells (CD3+, CD4+ and CD25high) were sorted to perform RNA sequencing. The categories （"sampleType" column in the SAMPLES section） contain PTC(CD8+ T cells from peripheral blood), NTC(CD8+ T cells from adjacent normal lung tissues) ,TTC (CD8+ T cells from tumor), PTH(CD3+, CD4+ and CD25- T cells from peripheral blood), NTH(CD3+, CD4+ and CD25- T cells from adjacent normal lung tissues), TTH(CD3+, CD4+ and CD25- T cells from tumor), PTR(CD3+, CD4+ and CD25high T cells from peripheral blood), NTR(CD3+, CD4+ and CD25high T cells from adjacent normal lung tissues), TTR(CD3+, CD4+ and CD25high T cells from tumor), PTY(CD3+, CD4+ and CD25mediate T cells from peripheral blood), NTY(CD3+, CD4+ and CD25mediate T cells from adjacent normal lung tissues), TTY(CD3+, CD4+ and CD25medate T cells from tumor).  Raw data access provided at: European Genome-phenome Archive (EGA) under accession EGAS00001002430

first: Xinyi

last: Guo

first: Yuanyuan

last: Zhang

first: Liangtao

last: Zheng

first: Chunhong

first: Jintao

last: Song

first: Qiming

first: Boxi

last: Kang

first: Zhouzerui

last: Liu

first: Rui

last: Xing

first: Ranran

last: Gao

first: Lei

first: Minghui

last: Dong

first: Xueda

last: Hu

first: Xianwen

last: Ren

first: Helge

last: Gottfried Roider

first: Tiansheng

last: Yan

first: Zemin


title: Slfn2 Regulates Type I Interferon Responses by Modulating the NFĸB Pathway

status: Public on Jun 26 2018

city: CHICAGO

first: Mariafausta

last: Fischietti

state: ILLINOIS

address: 303 E. Superior Street

department: Hematology/Oncology Robert H Lurie Comprehensive Cancer Center

country: USA

institute: Northwestern University

summary: We demonstrate that Slfn2 interacts with protein phosphatase 6 regulatory subunit 1 (PPP6R1), leading to reduced type I IFN-induced activation of nuclear factor kappa B (NFĸB) signaling, resulting in reduced expression of ISGs.

overall_design: Slfn2 WT and Slfn2 KO mouse embryonic fibroblasts (MEFs) were plated in triplicate/duplicate and were left untreated or were treated for 6 hours with 5x103 IU/ml of mouse IFNβ, followed by total RNA isolation. Directional libraries were prepared using Illumina TruSeq Stranded Total RNA HT Sample Prep Kit.

first: Leonidas

middle: C

last: Platanias


title: POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer [RNA-seq]

city: Cold Spring Harbor

first: Olaf

last: Klingbeil

state: New York

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

summary: Transcriptome analysis by high throughput sequencing

overall_design: Gene expression profiles in SCLC with gene knockout

first: Yu-Han

last: Huang

first: Christopher

last: Vakoc


title: POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Chromatin immunoprecipitation analysis by high throughput sequencing

overall_design: ChIP-seq data in SCLC cell lines


title: Neurotropism and Neurotoxicity Comparison among Retrograde Viral Tracers and Their Combinational Application in High-order Circuit Tracing

status: Public on Jun 23 2018

city: wuhan

first: Gang

last: Cao

state: hubei

address: Lion Rock One

institute: Huazhong Agricultural University

summary: Here, we demonstrated the neurotropism of different retrograde viral tracers are distinct through parallel comparison of multi-synaptic and mono-synaptic tracers in circuit tracing. By virture of their distinct tropism, we reconstructed more comprehensive LHA input circuit map. Notably, exogenous expression of TVA receptor in rabies virus (RV) resistant neurons can enable the infection of EnVA-pseudotyped RV. The potential viral receptor candidates attributing to neurotropism were analyzed by single cell sequencing. Further, we systematically compared neurotoxicity of glycoprotein-deleted RV and rAAV2-retro by RNAseq and immunohistochemistry. Finally, we demonstrated a proof-of-concept strategy for high-order circuit tracing by combining different viral tracers.

overall_design: Neurotropism and neurotoxicity comparison of different retrograde viral tracers and their combinational application in high-order circuit tracing

first: Weiming

last: Li

first: Weize

last: Xu

first: Yanyan

last: Zou


title: Methylation profile of neuroendocrine prostate cancer models

city: New York

first: Himisha

last: Beltran

address: 413 East 69th Street

institute: Weill Cornell Medicine

type: Methylation profiling by high throughput sequencing

summary: Our study represents a detailed molecular analysis of neuroenedocrine prostate cancer models

overall_design: Understanding the global methylation profile of tumor organoids and PDOXs.

first: Loredana

last: Puca


title: Neuroendocrine prostate cancer models

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

overall_design: Refer to individual Series


title: DNase-seq from kidney glomerular epithelial cell (ENCSR136KEL)

status: Public on Jun 21 2018

city: Stanford

first: ENCODE

last: DCC

state: CA

address: 300 Pasteur Dr

institute: ENCODE DCC

summary:
Genome-wide chromatin accessibility profiling of primary human glomerular and kidney cortex tubular outgrowth cultures

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


title: Molecular characterization of neuroendocrine prostate cancer organoids and PDOX by RNA-seq

summary: We report the generation and characterization of tumor organoids and PDOX derived from needle biopsies of metastatic lesions from neuroendocrine prostate cancer patients.

overall_design: Understanding the expression profile of neuroendocrine prostate cancer tumor organoids and PDOXs.

first: Rohan

last: Bareja

first: Andrea

last: Sboner


title: CRISPR/Cas9-targeted removal of unwanted sequences from small-RNA sequencing libraries

city: Huntsville

first: Richard

middle: M

last: Myers

state: AL

address: 601 Genome Way

institute: HudsonAlpha Institute for Biotechnology

type: Non-coding RNA profiling by high throughput sequencing

summary: In our study, we generated and sequenced small RNA libraries from commercially available brain total RNA or human blood plasma samples.  These samples were generated with MAD-DASH, a method we developed employing CRISPR/Cas9 ribonucleoprotein targeting specific overabundant sequences such as adapter dimer or miRNAs to reduce these sequences from final libraries. We sequenced treated and untreated samples to demonstrate specificity, efficacy, and reproducibility of our MAD-DASH small-RNA sequencing protocol.

overall_design: There are 42 fastq files in this submission, consisting of 12 fastqs from gel extracted small-RNA samples from human brain total RNA, 12 fastqs from bead cleanup (no gel extraction) small-RNA samples from human brain total RNA, and 18 fastqs from gel extracted small-RNA samples generated from human plasma RNA. Samples were  performed in replicate (n=2 for brain RNA samples, n=3 for plasma RNA samples) with either no MAD-DASH CRISPR treatment, or MAD-DASH CRISPR treatment targeting either adapter-dimer, specific miRNAs, or a combination of adapter dimer and miRNAs. Also included is a count table after read processing.

first: Andrew

middle: A

last: Hardigan


title: POU2F3 is a master regulator of a tuft cell-like variant of small cell lung cancer


title: DNase-seq from kidney tubule cell (ENCSR175IWT)


title: DNase-seq from glomerular visceral epithelial cell (ENCSR432SZT)


title: Transcriptome of human decidual cells treated by siRNA targeting FOXO1

city: West Haven

first: Cong

last: Liang

address: 300 Heffernan Dr.

institute: Yale University

summary: Here we report the gene expression profile of in vitro cultured human endometrial stromal cells treated with siRNA targeting FOXO1 piror to eutherian differentiation media exposure. The eutherian differentiation media contains cyclic AMP (cAMP) analogue 8-Br-cAMP and the progesterone (P4) analogue medroxyprogesterone acetate (MPA).

overall_design: RNA-seq on decidualizing human endometrial stromal cells treated with siRNA targeting FOXO1.

first: Mauris

last: Nnamani

first: Jamie

middle: D

last: Maziarz

first: Gunter

middle: P

last: Wagner


title: RNAseq of CD31-/CD45- pneumocytes after 4 weeks of KRasG12V activation by tamoxifen

city: MADRID

first: ROBERTO

last: MARTIN-HERNANDEZ

address: CANTOBLANCO

department: BIOSTATISTICS AND BIOINFORMATICS UNIT

institute: IMDEA ALIMENTACION

summary: We report the RNAseq data obtained from 50.000-100.000 CD31-/CD45- pneumocytes isolated by FACS from mice harboring a normal dose or one extra copy of the Sirt1 gene, and a tamoxifen-inducible oncogenic KI alelle of KRasG12V after 4 weeks of tamoxifen treatment. Pneumocytes with the activated form of the inducible KRasG12V oncogene sere selected making use of the reporter gene LacZ (located next to the oncogene in the same polycistronic mRNA), by loading CD31-/CD45- pneumocytes with the LacZ-activated fuorogenic molecule FDG prior to FACS sorting.

overall_design: Four replicates of each genetic group (Sirt1-WT and Sirt1-Tg) pneumocytes were used for this study. Sirt1-WT were used as reference controls.

first: Pablo

middle: J

last: Fernandez-Marcos

first: Roberto

last: Martin-Hernández

first: Luis

middle: F

last: Costa-Machado


title: A systematic p53 mutation library links differential functional impact to cancer mutation pattern and evolutionary conservation

city: Rehovot

first: Eran

last: Kotler

address: 234 Herzl st.

country: Israel

institute: Weizmann Institute of Science

summary: The TP53 gene is frequently mutated in human cancer. Research has focused predominantly on six major “hotspot” codons, accounting for only ~30% of cancer-associated p53 mutations. To comprehensively characterize the consequences of the p53 mutation spectrum, we created a synthetically designed library and measured the functional impact of ~10,000 DNA-binding domain (DBD) p53 variants in human cells in culture and in vivo. Our results highlight the differential outcome of distinct p53 mutations in human patients and elucidate the selective pressure driving p53 conservation throughout evolution. Furthermore, while loss of anti-proliferative functionality largely correlates with the occurrence of cancer-associated p53 mutations, we observe that selective gain-of-function may further favor particular mutants in vivo. Finally, when combined with additional acquired p53 mutations, seemingly neutral TP53 SNPs may modulate phenotypic outcome and presumably tumor progression.

overall_design: A synthetic library of 9,833 TP53 DNA-binding domain (DBD) sequence variants, composed of 4 sub-libraries (DBDA, DBDB, DBDC and DBDD) was expressed in human cells (H1299) and the relative fitness endowed by each variant was measured in a pooled time-course competition assay. For sub-libraries DBDA and DBDB, a biological replicate was performed. A similar experiment was performed with sub-library DBDD in HCT116 cells. In addition, the relative enrichment of these variants (DBDD expressed in HCT116 cells) was further measured in vivo (cells subcutaneously injected into mice) as well as in a 3D culture spheroid setting (using a small-scale library).

first: Odem

last: Shani

first: Guy

last: Goldfeld

first: Maya

last: Lotan-Pompan

first: Ohad

last: Tarcic

first: Anat

last: Gershoni

first: Thimas

last: Hopf

first: Debora

middle: S

last: Marks

first: Moshe

last: Oren

last: Segal


title: Charaterization of the molecular impacts of one week high fructose diet in human skeletal muscle

status: Public on Jun 24 2018

city: Pierre Bénite

first: emmanuelle

last: meugnier

address: Cens Eli Bat 2 D- Hopital Lyon Sud

country: France

summary: The adaptive mechanisms in response to excess energy supply are still poorly known in humans. Our aims were to define metabolic responses and changes in gene expression in skeletal muscle of healthy offsprings of type 2 diabetic patients during  one week of high fructose diet.

overall_design: Offsprings of type 2 diabetic patient subjects were submitted to a high fructose diet during 7days. Muscle biopsies were taken at Day 0 and Day 7.

first: Emmanuelle

last: Meugnier

first: Martine

last: Laville

first: Hubert

last: Vidal

first: Luc

last: Tappy


title: ICAM-1 deficiency in the bone marrow niche impairs quiescence and repopulation of hematopoietic stem cells

city: Guangzhou

first: Lingyun

last: Zheng

state: Guangdong

address: 280 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center

department: School of Life Sciences and Biopharmaceutics

institute: Guangdong Pharmaceutical University

summary: The bone marrow niche plays a critical role in controlling the fate of hematopoietic stem cells (HSCs) by integrating intrinsic and extrinsic signals. However, the molecular events in the HSC niche remain to be investigated. Here, we report that intercellular adhesion molecule-1 (ICAM-1) maintains HSC quiescence and repopulation capacity in the niche. ICAM-1-deficient mice (ICAM-1-/-) displayed significant expansion of phenotypic long-term HSCs with impaired quiescence, as well as favors myeloid cell expansion. ICAM-1-deficient HSCs presented normal reconstitution capacity during serial transplantation; however, reciprocal transplantation experiments showed that ICAM-1 deficiency in the niche impaired HSCs quiescence and repopulation capacity. In addition, ICAM-1 deletion caused failure to retain HSCs in the bone marrow and changed the expression profile of stroma cell-derived factors, possibly representing the mechanism for defective HSCs in ICAM-1-/- mice. Collectively, these observations identify ICAM-1 as a regulator in the bone marrow niche.

overall_design: WT donor LSK (Ly5.1+) were sorted after transplanted into WT (n=3) or ICAM-1-/- (n=3) recipients (Ly5.2+) for 8 weeks, we analysis the transcriptional profile of LSK hematopoietic stem cells after transplantation by High-throughput RNA-sequencing.

first: Bin

last: Zou

first: Yu-feng

last: Liu


title: Microarray gene expression profiling in colorectal (HCT116) and hepatocellular (HepG2) carcinoma cells treated with Melicope ptelefolia leaf extract reveals transcriptome profiles exhibiting anticancer activity

city: Kuala Lumpur

first: Johari

last: Mohd Ali

state: WP

address: Lembah Pantai

department: Department of Molecular Medicine

country: Malaysia

institute: University of Malaya

summary: Microarray whole-transcriptome profiling in HCT116 and HepG2 cells treated with Melicope ptelefolia leaf extract reveals transcriptome profles exhibiting anticancer activity

overall_design: HepG2 and HCT116 cells were treated for 24 hr with Melicope ptelefolia hexane leaf extract (MP-HX) at 60 µg/mL for HCT116 and 78 µg/mL. RNA was extracted and subjected to microarray whole transcriptome profiling utilizing Human Gene (HuGene) 2.0 ST array (Catalogue No. 902499, Applied Biosystem).

first: Mohammad

last: Faujul Kabir


title: Determination of global decay rates of yeast transcriptome and identification of factors impact mRNA stability

city: Cleveland

first: Jeff

last: Coller

state: OH

address: 10900 Euclid Ave

department: Center for RNA Science and Therapeutics

institute: Case Western Reserve University

summary: In this work, we determine total mRNA decay rates in rpb1-1 and rpb1-1/caf1∆ cells, calculate half-lives in rpb1-1/caf1∆ cells relative to rpb1-1 cells and correlate them with codon optimality.

overall_design: mRNA profiling was done on 10 time points in rpb1-1/caf1 cells and sequenced using a paired end protocol on an Illumina HiSeq2000 instrument. A biological duplicate was performed.


title: expression data from NDRG1 depleted SKBR3 cells

city: Rensselaer

first: Sridar

middle: V

last: Chittur

state: NY

address: One Discovery Drive, CRC 342G

department: Center for Functional Genomics

institute: SUNY-University at Albany

summary:
SKBR3 cells expressing NDRG1 shRNA1 or vector control were harvested by trypsinization and total RNA was extracted.  Silencing NDRG1 reduces cell proliferation rates, causing lipid metabolism dysfunction including increased fatty acid incorporation into neutral lipids and lipid droplets.
global changes in transcriptome due to NDRG1 silencing were observed

overall_design: Three SKBR3 GFP shRNA expressing cultures (control), SKBR3 G8 (shNDRG1) shRNA expressing cultures. Cells were grown in DMEM 10% FBS and harvested in log phase.

first: Christopher

last: Sevinsky

first: Douglas

last: Conklin


title: Effect of Notch Signaling Inhibitor on Gene Expression in Lipopolysaccharide-stimulated Macrophages in the Presence of Immune Complex

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

summary: Lipopolysaccharide (LPS)/immunue complex (IC) stimulated macrophages produce cytokine profiles that differe from LPS-stimulated inflammatory macropahges. Notch signaling is activated in LPS/IC-stimulated macrophages and inhibition of Notch signaling reduced IL-10 production. This study investigated the effect of gamma-secretase inhibitor (GSI) that suppresses Notch signaling pathway, on gene expression profiles in macrophages activated by LPS/IC.

overall_design: Gamma secretase inhibitor (GSI)-treated bone marrow derived macrophage mRNA profiles were generated by deep sequencing using Illumina NextSeq 500. The results were compared between vehicle control (dimethylsulfoxide)-treated cells and GSI-treated cells.

first: Pornrat

last: Kongkavitoon

first: Patarin

last: Tangtanatakul

first: Wipawee

last: Wongchana

first: Pinidphon

last: Prombutara


title: TCR-MHC Interaction Strength Defines Trafficking and Resident Memory Status of CD8 T cells in the Brain.

city: London

first: Eva

last: Frickel

address: 1 Midland Road

department: Host-Toxoplasma Interaction Laboratory

country: United Kingdom

institute: The Francis Crick Institute

summary: It is unknown how peptide-activated CD8 T cells that harbour different and distinct T cell receptors to the same MHC-epitope combination differ in terms of their transcriptional expression profile.

overall_design: In this experiment we compared the expression profile of three activated transnuclear CD8 T cell clones that differ in their T cell receptor and affinity to cognate peptide and self-reactivity. We find that the transcriptomes of these T cells differ with respect to readiness for cell cycle progression and T cell receptor signaling. The transnuclear mice harbouring the CD8 T cells were reported in Kirak et al, Science, 2010 and characterised in Swee et al, Open Biology, 2016. In brief, the TCR sequence can be found in the former publication, the TCR affinity hierarchy to cognate peptide is defined in the latter paper as R7-I>R7-III>R7-II. The self-reactivity hierarchy can be found in the latter paper as well (defined by CD5 and Nur-77 expression) and is R7-III>R7-I>R7-II.

first: Anna

last: Sanecka

first: Nagisa

last: Yoshida

first: Elizabeth

last: Kolawole

first: Harshil

last: Patel

first: Brian

last: Evavold

first: Eva-Maria


title: LSD1 ablation stimulates anti-tumor immunity and enables checkpoint blockade

city: Hangzhou

first: Wanqiang

last: Sheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Department of Immunology

institute: Zhejiang University School of Medicine

summary: Chromatin regulators play a broad role in regulating gene expression, and when gone awry, can lead to cancer. Here we demonstrate that ablation of the histone demethylase LSD1 in cancer cells increases repetitive element expression, including ERVs, and decreases expression of RNA-induced silencing complex (RISC) components. Significantly, this leads to dsRNA stress and activation of type 1 interferon, which stimulates anti-tumor T cell immunity and restrains tumor growth. Furthermore, LSD1 depletion enhances tumor immunogenicity and T cell infiltration in poorly immunogenic tumors, and elicits significant responses of checkpoint blockade-refractory mouse melanoma to anti-PD-1 therapy. Consistently, TCGA data analysis shows an inverse correlation between LSD1 expression and CD8+ T cell infiltration in various human cancers. Our study identifies LSD1 as a potent inhibitor of anti-tumor immunity and responsiveness to immunotherapy, and suggests LSD1 inhibition combined with PD-(L)1 blockade as a novel cancer treatment strategy.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Gene expression profiling of in vitro control and LSD1 KD MCF-7 cells (in biological replicates), as well as ex vivo scramble, LSD1 KO and LSD1/MDA5 DKO B16 tumor cells (in biological triplicates) was analyzed by RNA-seq. Genomic occupancy of LSD1, H3K4me1 and H3K4me2 in in vitro control and LSD1 KD MCF-7 cells, as well as ex vivo scramble and LSD1 KO B16 tumor cells was analyzed by ChIP-seq.

first: Yang

last: Shi

first: Sujun

last: Chen

first: Housheng

last: He


title: Genome-wide maps of PRDM16 binding sites and histone modifications  [H3K4meChIP-Seq]

city: Boston

first: Corey

last: Harwell

state: MA

address: 200 Longwood Avenue

department: Neurobiology

institute: Harvard Medical School

summary: Identification of genome-wide PRDM16 binding, H3K27ac and H3K4me in WT and Prdm16 conditional knock-out (cKO) mouse (Emx1Ires-Cre; Prdm16flox/flox) at embryonic day 15.5.

overall_design: Whole cortex lysates were used in ChIP-seq experiments to identify PRDM16 binding (2 replicates per genotype), H3K27ac (3 replicates per genotype) and H3K4me (2 replicates per genotype) in WT and Prdm16 cKO brains.

first: José-Manuel

last: Baizabal


title: Genome-wide maps of PRDM16 binding sites and histone modifications  [H3K27Ac ChIP-Seq]


title: miRNA expression profiles of HeLa-Cas9 and NCI-N87 cells

city: Duarte

first: Ren-Jang

last: Lin

address: 1500 E Duarte Rd

department: Molecular and Cellular Biology

institute: City of Hope

summary: MicroRNAs (miRNAs) play an important role in the regulation of gene expression and are often dysregulated in disease. The recent development of the CRISPR-Cas9 gene-editing system, composed of the Cas9 nuclease in complex with a single guide RNA (sgRNA), allows researchers to direct DNA cleavage at a predetermined site and to conduct genome-scale knockout screens. To determine the functional role of miRNAs in cancer, we designed and constructed a library of 7,382 sgRNAs to target 85% of the 1,881 annotated human miRNA stem-loops. We then examined the role of miRNAs in HeLa cell fitness by monitoring the change in frequency of each sgRNA over time. We identified 44 pro-proliferative miRNAs from two replicate experiments, including miR-31, a known cervical cancer overexpressing miRNA that enhances HeLa cell proliferation. We also examined the role of miRNAs in NCI-N87 gastric cancer cells and identified 10 pro-fitness and 10 anti-fitness miRNAs. In both screens, many of the pro-fitness miRNAs identified are overexpressed in tumors cervical tumors for HeLa or gastric tumors for NCI-N87. In summary, we present a CRISPR miRNA-targeted screen which was able to identify both known and novel fitness-associated miRNAs in the HeLa and NCI-N87 cell lines.

overall_design: The miRNA expression profile of NCI-N87 gastric cancer cells was determined by high throughput miRNA sequencing (NCI-N87_miR-seq). To determine the miRNA expression profile of the clonal HeLa-Cas9 cell line, we determined the miRNA expression in HeLa-Cas9 cells 9 days after transduction with the LX-miR library for two biological replicates (HeLa_1D7_miR-seq and HeLa_2D7_miR-seq). To examine the impact of doxycycline treatment on miRNA expression, we also profiled the miRNA expression in HeLa-Cas9 cells with (HeLa_1D22G1_miR-seq) and without (HeLa_1D22md_miR-seq) doxycycline treatment.

first: Jessica

last: Kurata


title: Genome-wide maps of PRDM16 binding sites and histone modifications

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


title: Transcriptome profiling of WT and Prdm16 mutant cells in embryonic mouse cerebral cortex.

summary: Transcriptome profiling of radial glia, intermediate progenitors, and cortical neurons in WT and Prdm16 conditional knock-out (cKO) mouse (Emx1Ires-Cre; Prdm16flox/flox) at embryonic day 15.5.

overall_design: Sorting of PAX6+ radial glia, TBR2+ intermediate progenitors and Pax6-TBR2- neurons from WT and Prdm16 cKO embryonic cerebral cortex was followed by library preparation and RNA-seq of 4 biological replicates per cell type and genotype.


title: Capturing the onset of PRC2-mediated repressive domain formation[ChIP-Seq, 3]

first: Danny

last: Reinberg

address: 522 First Avenue

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

summary: Our study defines nucleation and spreading regions for Polycomb repressive complex 2 (PRC2), demonstrating the principle of PRC2 domain formation in mammals. We elucidate the role of genome architecture in formation of these domains and identify JARID2 and MTF2 as being crucial for full recruitment of PRC2 to chromatin.

overall_design: In this experiment, we performed ChIP-seq with the indicated antibodies and genotpyes of mESCs.

first: Ozgur

last: Oksuz

first: Varun

last: Narendra

first: Chul-Hwan

last: Lee

first: Nicolas

last: Descostes

first: Gary

last: LeRoy

first: Ramya

last: Raviram

first: Lili

last: Blumenberg

first: Kelly

last: Karch

first: Pedro

middle: R

last: Rocha

first: Benjamin

last: Garcia

first: Jane

last: Skok


title: Genome-wide maps of PRDM16 binding sites and histone modifications [PRDM16 ChIP-Seq]


title: Next Generation Sequencing Analysis of Wild Type, ADAR2 over expressing and ADAR2+SRSF9 overexpresssing HEK 293T cells Transcriptomes

city: Singapore

first: Meng How

last: Tan

address: 60 Biopolis Street, Genome Building #02-01

country: Singapore

institute: Genome Institute of Singapore

summary:
Purpose: A-to-I RNA editing is critical for many cellular processes. The sites of A-I RNA editing can be identified through RNA-seq and matching the reads to the annotated database like RADAR. The goals of this study is to compare A-I RNA editing profile among wild type, ADAR2 overexpressing and ADAR2+SRSF9 overexpressing 293T cells to evaluate the influence of SRSF9 repressive  action on A-I RNA editing
Methods: A-I RNA editing profile and gene expression profiles were generated by deep sequencing from all the samples, using  NEBNext® Ultra™ Directional RNA Library Prep Kit. The sequence reads that passed quality filters were analyzed for identifying the A-I RNA editing sites using RADAR Database
Results: Upon overexpression of ADAR2, we found that 18,174 sites were differentially edited compared to control cells, of which 97.0% showed a significant increase in their editing levels as expected (P < 0.05, Fisher’s test). Furthermore, when we overexpressed both ADAR2 and SRSF9 together, we found that 6,994 sites were differentially edited compared to overexpression of the deaminase alone (P < 0.05, Fisher’s test). Importantly, the editing of 92.5% of these sites was down-regulated, consistent with the function of SRSF9 as a repressor of editing.
Conclusions: Our study reports a detailed analysis of the effect of SRSF9 on A-I RNA editing of ADAR2-specific targets. We Conclude that this SRSF9 regulon is significantly enriched for brain-specific editing sites despite our unbiased approach.

overall_design: This study illustrates the effect of SRSF9 on A-I RNA editing of ADAR2 specific target sites

first: Tan

last: How

first: Raghuvaran

last: Shanmugam

first: Zhan

last: Fang


title: Next Generation Sequencing Analysis of Wild Type, ADAR2 over expressing and ADAR2+SRSF9 overexpresssing SH-Sy5y cells Transcriptomes


title: CXCL12/CXCR4 signaling enhances human PSC-derived hematopoietic progenitor function and overcomes early in vivo transplantation failure

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

summary: Human pluripotent stem cells (hPSC) generate hematopoietic progenitor cells (HPC), but fail to engraft xenograft models, which is a hallmark feature of adult/somatic hematopoietic stem cells (HSC) from human donors. Progress to derive hPSC-derived HSCs has relied on cell autonomous approaches that force expression of transcription factors (TF), however the role of bone marrow (BM) niche remains poorly understood. Here, we quantified a failure of hPSC-HPCs to survive even in the first 24 h upon transplantation into the BM. Across several hPSC-HPC differentiation methodologies, we identified the lack of CXCR4 expression and network function. Ectopic CXCR4 conferred CXCL12-dependent signaling of hPSC-HPCs in biochemical assays and increased migration/chemotaxis and progenitor capacity, as well as survival and proliferation following transplantation in vivo. In addition, hPSC-HPCs forced to express CXCR4 demonstrated a transcriptional shift toward somatic HPCs, but this approach failed to produce long-term HSC engraftment. Our results reveal that independent of differentiation methods, networks involving CXCR4 should be targeted to generate HSCs with in vivo function from hPSCs.

overall_design: Human pluripotent stem cell (hPSC) derived hematopoietic progenitor cells (HPC) were generated using previously described methods; Cytokines & BMP4 (Chadwick et al. Blood 2003) and endothelial-to-hematopoietic transition (EHT) (Lee et al. The Journal of Clinical Investigation 2017). Lentiviral was used to achieve CXCR4+ hPSC-HPCs, differentiated as previously described (Chadwick et al. Blood 2003). Adult/somatic HPCs were isolated from bone marrow, cord blood, and mobilized peripheral blood.

first: Jennifer

last: Reid

first: Borko

last: Tanasijevic

first: Diana

last: Golubeva

first: Zoya

last: Shapovalova


title: Differences in cell cycle status underlie transcriptional heterogeneity in the HSC compartment

city: Copenhagen

first: Nicolas

last: Rapin

address: Ole Maaloes vej 5

department: Finsen Laboratory

country: Denmark

institute: Copenhagen University

summary: Hematopoietic stem cells (HSCs) are considered a heterogeneous cell population. In an attempt to further resolve the HSC compartment, we characterized a retinoic acid (RA) reporter mouse line. Sub-fractionation of the HSC compartment in RA-CFP reporter mice demonstrated that RA-CFP-dim HSCs were largely non-proliferative and displayed superior engraftment potential in comparison to RA-CFP-bright HSCs. Gene expression analysis demonstrated higher expression of RA-target genes in RA-CFP-dim HSCs, contrasting the RA-CFP reporter expression, but both RA-CFP-dim and –bright HSCs responded efficiently to ATRA in vitro. Single-cell RNA-sequencing of >1,200 HSCs showed that differences in cell cycle activity constitutedthe main driver of transcriptional heterogeneity in HSCs. Moreover, further analysis of the single-cell RNA-seq data revealed that stochastic low-level expression of distinct lineage-affiliated transcriptional programs is a common feature of HSCs. Collectively, this work demonstrates the utility of the RA-CFP reporter line as a tool for the isolation of superior HSCs.

overall_design:
- Whole genome bisulphite sequencing of approximately 1000 CFP dim HSCs versus CFP bright HSCs were generated in duplicates, using Illumina Next Seq 500.
- RNA-seq of HSCs.
- Single cell RNA-seq of HSCs.

first: Bo

middle: T

last: Porse

first: Felicia

middle: K

last: Lauridsen

first: Tanja

middle: L

last: Jensen


title: Transcriptome-wide map of SRSF9 bining in the presence and absence of ADAR2 in HEK293T cells

summary: Here, we show that the splicing factor SRSF9 selectively controls the editing of many brain-specific sites in mammals. SRSF9 is more lowly expressed in the mammalian brain than in non-brain tissues. Gene perturbation experiments and minigene analysis of candidate sites demonstrated that SRSF9 could robustly repress A-to-I editing by ADAR2. We found that SRSF9 biochemically interacted with ADAR2 in the nucleus via its RRM2 domain alone. Additionally, this interaction required the presence of the RNA substrate and disrupted the formation of ADAR2 dimers. Using transcriptome-wide location analysis and genome-wide RNA profiling, we identified 1,328 editing sites that are regulated directly by SRSF9. Importantly, we showed that this SRSF9 regulon is significantly enriched for brain-specific editing sites despite our unbiased approach. We further provide evidence that SRSF9 prevents cells from undergoing apoptosis possibly through the inhibition of ADAR2-mediated editing. Collectively, our results highlighted the importance of SRSF9 as an editing regulator and suggested that other splicing factors may also be involved in regulating RNA editing.

overall_design: Elucidting the repressive action of SRSF9 on the ADAR2 targets


title: Ligand-insensitive PPARγ controls progressive or reinforcing macrophage polarization as an epigenomic ratchet of transcriptional memory [ChIP-seq]

status: Public on Jun 20 2018

city: South San Francisco

first: Bence

last: Daniel

address: 1 DNA Way

department: Department Proteomic and Genomic Technologies

institute: Genentech Inc.

summary: Macrophages change their phenotype in response to complex (reinforcing or opposing) environmental cues. The molecular components providing the epigenomic basis of progressive or reinforcing polarization are largely unknown. Here we show that the normally ligand-activated nuclear receptor, Peroxisome Proliferator-Activated Receptor gamma (PPARγ), is a predominantly ligand-insensitive, epigenomic driver of a robust phenotypic change in macrophages uniquely upon repeated/reinforcing IL-4 stimulation. Ligand-insensitive PPARγ recruits P300, RAD21 and establishes a permissive chromatin environment, conferring transcriptional memory by facilitating the binding of STAT6 and RNAPII leading to more robust eRNA production upon IL-4 restimulation. PPARγ-mediated transcriptional memory allows the progressive, functional transition of macrophages upon repeated cytokine exposure by controlling the expression of an extracellular matrix remodeling related gene network, also expressed in macrophages from a mouse model of muscle regeneration and show progressive upregulation during the course of regeneration after muscle injury, coinciding with the appearance of IL-4 and PPARγ. Collectively, in contrast to the current prevailing view, alternative polarization gives rise to a predominantly ligand-insensitive PPARγ:RXR cistrome, regulating progressive/reinforcing macrophage polarization.

first: Laszlo

last: Nagy


title: Ligand-insensitive PPARγ controls progressive or reinforcing macrophage polarization as an epigenomic ratchet of transcriptional memory [RNA-Seq]


title: Ligand-insensitive PPARγ controls progressive or reinforcing macrophage polarization as an epigenomic ratchet of transcriptional memory [RNA-Seq2]


title: Ligand-insensitive PPARγ controls progressive or reinforcing macrophage polarization as an epigenomic ratchet of transcriptional memory

overall_design: Refer to individual Series


title: Medullary breast carcinoma, a triple-negative breast cancer subtype associated with BCLG overexpression.

city: Paris Cedex 05

first: Cecile

last: Laurent

address: 26 rue d'ulm

institute: Institut Curie

summary: Gene expression was compared between medullary breast carcinoma (MBC) and non medullary basal-like breast carcinoma (non-MBC BLC).

overall_design: The transcriptome of 19 MBC and 34 non-MBC BLC were analyzed using Affymetrix U133plus2 Arrays.

first: Pierre

last: Romero

first: Vanessa

last: Benhamo

first: Gabrielle

last: Deniziaut

first: Laetitia

last: Fuhrmann

first: Frédérique

last: Berger

first: Elodie

last: Manié

first: Jaydutt

last: Bhalshankar

first: Cécile

first: Sophie

last: Vacher

first: Elisabetta

last: Marangoni

first: Nadège

last: Gruel

first: Gaetan

last: MacGrogan

first: Fabien

last: Reyal

first: Roman

last: Rouzier

first: Olivier

last: Delattre

first: Tatiana

last: Popova

first: Marc-Henri

last: Stern

first: Dominique

last: Stoppa-Lyonnet

first: Ivan

last: Bièche

first: Anne

last: Vincent-Salomon


title: Continuous-trait probabilistic model for comparing multi-species functional genomic data

city: Pittsburgh

first: Yang

last: Yang

state: PA

address: 5000 Forbes Ave

department: Computational Biology

institute: Carnegie Mellon University

summary: We developed a probabilistic method to simultaneously infer genome-wide heterogeneous evolutionary states. We applied the proposed method to analyze a cross-species DNA replication timing (RT) dataset from the same cell type in five primate species.  We demonstrated that the proposed model enables discovery of genomic regions with distinct evolutionary patterns of RT.

sample_organism:
Chlorocebus aethiops
Pan troglodytes
Pongo pygmaeus
Homo sapiens
Nomascus leucogenys

overall_design: Comparing replication timing profile among 5 primate species

first: Quanquan

last: Gu

last: Zhang

first: Takayo

last: Sasaki

first: Julianna

last: Crivello

first: Yuchuan

last: Wang

first: Rachel

last: O'Neill

first: David

last: Gilbert

first: Jian

last: Ma


title: Medullary breast carcinoma, a triple-negative breast cancer subtype associated with BCLG overexpression and BRCAness

first: Cecile

last: Laurent

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


title: ADAR2 in HEK293T cells

first: Meng How

last: Tan


title: mRNA profiles of active hematopoieitc stem cells

city: Kumamoto

first: Terumasa

last: Umemoto

address: 2-2-1, Honjo, Chuo-Ku

country: Japan

institute: Kumamoto University

summary:
Purpose: The goals of this study are to elucidate the underlying mechanism for the activation of HSCs
Methods: After wild type (WT) HSCs  (CD150+ CD48- EPCR+ Lineage-) were treated with 5-fluorouracil (5-FU), 100 cells of HSCs were sorted.   Moreover, after the culture with or without Nifedipien,  cultured HSC fraction  (CD150+ CD48- EPCR+ c-kit+ Sca-1+ Lineage-) were sorted. These cells were subjected to mRNA sequence using Next-seq (n>3). The sequence reads that passed quality filters were analyzed by CLC genomic workbench.

overall_design:
After the culture with or without Nifedipine, HSCs wihtin 3 cell division population were sorted, and subsequently mRNA profiles were generated by deep sequencing using Next-seq (n>3).
Using HSCs derived from untreated and 5-FU-treated mice, mRNA profiles were generated by deep sequencing using Next-seq (n>4).

first: Toshio

last: Suda


title: Chromatin remodeler CHD8 in CNS myelination and remyelination

city: Cincinnati

first: Richard

last: Lu

address: 3333 Burnet Ave

department: CBDI

institute: Cincinnati Children's Hospital Medical Center

summary: Mutations in CHD8, an ATP-dependent chromodomain-helicase-DNA-binding protein 8, are known to cause a set of Autism Spectrum Disorders (ASD). We found that CHD8 is highly expressed in myelinating oligodendrocytes (OL) and their progenitors in the developing central nervous system (CNS). We performed CHD8 chIP-seq analysis in cultured oligodendrocytes.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design:
11 samples:
RNA-seq:2 Control  Samples vs 2 cKO samples;
ChIP-seq: 2 Chd8samples, 1 chd7 sample;
H3K4me3 ChIP-seq: 1 control vs 1 Ch8cko;
ATAC-seq 1 control vs 1 Chd8cKO

first: Chuntao

last: Zhao


title: RNA sequencing and pathway analysis identify important pathways involved in hypertrichosis and intellectual disability in patients with Wiedemann-Steiner syndrome

status: Public on Jun 19 2018

city: Paris

first: Thierry

last: Bienvenu

address: 24 rue du faubourg St jacques

institute: INSERM

summary: RNAseq in Wiedemann Steiner syndrome

overall_design: examination of two cohorts of patients with or without KMT2A mutation

first: Léo

last: Mietton

first: Nicolas

last: Lebrun

first: Irina

last: Giurgea

first: Alice

last: Goldenberg

first: Benjamin

last: Saintpierre

first: Juliette

last: Hamroune

first: Alexandra

last: Afenjar

first: Pierre

last: Billuart


title: Ligand-insensitive PPARγ controls progressive or reinforcing macrophage polarization as an epigenomic ratchet of transcriptional memory [ATAC-seq]

first: Bence

last: Daniel

first: Laszlo

last: Nagy


title: Integrative analysis of single cell genomics data by coupled nonnegative matrix factorizations (ATAC-Seq)

city: Stanford

first: Zhana

last: Duren

address: 318 Campus Drive

institute: Stanford university

summary: 415 scATAC-seq samples generated for the retinoic acid-induced mESC differenation at day 4.

overall_design: We present a method(Coupled NMF) to cluster single cell chromatin accessibility data and single cell gene expression data simultaneously.

first: Xi

last: Chen

first: Mahdi

last: Zamanighomi

first: Wanwen

last: Zeng

first: Ansuman

last: Satpathy

first: Howard

middle: Y

last: Chang

first: Yong

last: Wang

first: Wing

last: Wong


title: Expression data from MSCs cultured on 3D and 2D matrixes

city: Beijing

first: Jing

last: Li

address: 28 Fuxing Road

institute: Chinese PLA General Hospital

summary:
MSCs in vivo have a markedly different three-dimensioanal (3D) niche compared to the traditional two-dimensional (2D) culture in vitro.
We used microarrays to detail  the global difference of gene expression between MSCs cultured on 3D and 2D matrixes

overall_design: Total RNA from each group (MSCs in 2D surface culture, MSCs in 3D collagen, chitosan, and PLGA matrixes) was analysed using gene microarrays

first: Tong

first: Xiahe

last: Huang

first: Jianwu

last: Dai


title: BET bromodomain dependency in EWS/ETS driven Ewing Sarcoma

city: PHILADELPHIA

first: Irfan

last: Asangani

address: 421 Curie Bld.

department: Cancer Biology

institute: University of Pennsylvania

summary: The pathognomonic EWS/ETS fusion transcription factors drive Ewing sarcoma (EWS) by orchestrating an oncogenic transcription program. Therapeutic targeting of EWS/ETS has not been successful; therefore identifying mediators of the EWS/ETS function could offer new therapeutic targets. Here we describe the dependency of chromatin reader BET bromodomain proteins in EWS/ETS driven transcription and investigate the potential of BET inhibitors in treating this lethal cancer. Similar to EWS/ETS fusions, knockdown of BET proteins BRD2/3/4 severely impaired the oncogenic phenotype of EWS cells. Notably, EWS/FLI1 and EWS/ERG was found to be in a transcriptional complex consisting of BRD4. RNA-Seq analysis upon BRD4 knockdown or its pharmacologic inhibition by the BET inhibitor JQ1 revealed an attenuated EWS/ETS transcriptional signature. In contrast to other reports, JQ1 reduced proliferation, and induced apoptosis through MYC-independent mechanism without affecting EWS/ETS protein levels, which was further confirmed by depleting BET proteins using PROTAC-BET degrader (BETd). Interestingly, polycomb repressive complex 2 (PRC2) associated factor PHF19 was downregulated by JQ1/BETd or BRD4 knockdown in multiple EWS cells. ChIP-seq analysis revealed occupancy of EWS/FLI1 at a distal regulatory element of PHF19 and its subsequent knockdown resulted in downregulation of PHF19 expression. Furthermore, deletion of PHF19 by CRISPR-Cas9 system lead to a decreased tumorigenic phenotype and increased sensitivity to JQ1. Importantly, PHF19 expression was associated with worse prognosis of Ewing sarcoma patients.  In vivo, JQ1 demonstrated anti-tumor efficacy in multiple mouse xenograft models of EWS. Together, these results indicate that EWS/ETS require BET epigenetic reader proteins for its transcriptional program including PHF19 expression, which can be mitigated by BET inhibitors. Moreover, this study provides a clear rationale for the clinical utility of BET inhibitors in treating Ewing sarcoma.

overall_design: Gene epxression by RNAseq in the ewing sarcoma cell lines with knockdown of EWS-FLI1, BRD4 or JQ1 treament, knockout of PHF19

first: Ram

last: Natesan


title: Single nucleus inDrops to profile adult human kidney

city: St. Louis

first: Haojia

last: Wu

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

overall_design: Single nuclei were isolated from adult human kidney and subjected to inDrops single cell RNA-seq

first: Benjamin

last: Humphreys


title: Transcriptional plasticity, priming and commitment in hematopoietic lineages

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

institute: Weizmann Institute of Science


title: H4K20me3 co-localizes with activating histone modifications at transcriptionally dynamic regions in embryonic stem cells

status: Public on Jun 18 2018

city: Detroit

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

summary: Bivalent chromatin domains consisting of the activating histone 3 lysine 4 trimethylation (H3K4me3) and repressive histone 3 lysine 27 trimethylation (H3K27me3) histone modifications are enriched at developmental genes that are repressed in embryonic stem cells but active during differentiation. However, it is unknown whether another repressive histone modification, histone 4 lysine 20 trimethylation (H4K20me3), co-localizes with activating histone marks in ES cells. Here, we describe the previously uncharacterized coupling of the repressive H4K20me3 heterochromatin mark with the activating histone modifications H3K4me3 and histone 3 lysine 36 trimethylation (H3K36me3), and transcriptional machinery (RNA polymerase II; RNAPII), in ES cells. These newly described bivalent domains consisting of H3K4me3/H4K20me3 are predominantly located in intergenic regions and near transcriptional start sites of active genes, while H3K36me3/H4K20me3 are located in intergenic regions and within gene body regions of active genes. Global sequential ChIP, also termed reChIP-Seq, confirmed the simultaneous presence of H3K4me3 and H4K20me3 at the same genomic regions in ES cells. Genes containing H3K4me3/H4K20me3 exhibit decreased RNAPII pausing and are poised for deactivation of RNAPII binding during differentiation relative to H3K4me3 marked genes. An evaluation of transcription factor (TF) binding motif enrichment revealed that DNA sequence may play a role in shaping the landscape of these novel bivalent domains. Moreover, H3K4me3/H4K20me3 and H3K36me3/H4K20me3 bound regions are enriched with repetitive LINE and LTR elements.

overall_design: reChIP-Seq and ChIP-Seq of undifferentiated murine ES cells


title: Epigenome analysis of Chinese Han male semen samples

city: Chengdu

first: Luyao

address: Fa Yi Building, No.16, Section 3, Renmin Nan Road, Chengdu, China

institute: Institute of Forensic Medicine, West China School of Basic Sciences and Forensic Medicine, Sichuan University

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of Chinese Han male semen samples. The Illumina Human Methylation 450 Beadchip was used to obtain DNA methylation profiles across approximately 450,000 CpGs. Samples included 3 young males (aged 24, 25 and 25 years old) and 3 aged males (aged 63, 60 and 55 years old).

overall_design: Bisulphite converted DNA isolated from semen of 6 males were hybridised to the Illumina Infinium HumanMethylation450 Beadchip.

first: Yiping

last: Hou

first: Mechthild

last: Prinz

first: Feng

last: Song

first: Jiayi


title: Ambient Pollution Related Reprogramming of the Human Small Airway Epithelial Transcriptome

city: New York

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: Epidemiological studies have demonstrated that exposure to particulate matter (PM) ambient pollution has adverse effects on lung health, exacerbated by cigarette smoking. Fine airborne particles <2.5 µm (PM2.5) are the most harmful of the urban pollutants, and the most closely linked to respiratory disease. Based on the knowledge that the small airway epithelium (SAE) plays a central role in pathogenesis of smoking-related lung disease, we hypothesized that elevated PM2.5 levels are associated with dysregulation of SAE gene expression.

overall_design: From 2009-2012, healthy nonsmoker (n=29) and smoker (n=129), residents of New York City (NYC) underwent serial bronchoscopy with SAE brushing (2.6 ± 1.3 procedures/subject, total of 405 samples) over 12 months. PM2.5 levels varied from 6.2-18 μg/m3. SAE gene expression was assessed by Affymetrix HG-U133_Plus_2 microarray. SAE gene expression was modeled as a linear function of 30-day mean NYC PM2.5 levels over the same time period. Significance was calculated by two-sided Wald test, reflecting the probability that the regression coefficient for the pollution variable was non-zero. PM2.5-related gene dysregulation was quantified using Benjamini-Hochberg correction. In non-smokers, there was no dysregulation associated with ambient PM2.5 levels. In marked contrast, n=180 genes were significantly dysregulated in association with PM2.5 levels in smokers.

first: Sarah

last: O'Beirne

first: Sushila

last: Sheenoy

first: Jacqueline

last: Salit

first: Robert

last: Kaner

first: Sudha

last: Visvanathan

first: Jay

last: Fine

first: Jason

last: Mezey

first: Ronald

last: Crystal


title: Differential expression analysis of miRNAs expressed in blood and CSF of Huntington's disease [miRNA-seq]

city: Boston

first: Xianjun

last: Dong

address: 60 Fenwood Rd

department: Neurology

institute: Brigham and Women's Hospital

summary: Huntington’s disease (HD) is an autosomal-dominant neurodegenerative disorder caused by the CAG expansion in the Huntingtin (HTT) gene. Several studies have shown the potential of microRNAs as biomarkers in neurodegenerative diseases. However, no bona fide microRNAs have been identified as promising diagnostic biomarkers for HD. As part of the PREDICT-HD project, here we performed NanoString on blood samples of 115 pre-manifest HD cases and 111 controls in an effort to provide promising biomarkers for the diagnostic of HD or the disease processes tracking. The results showed that five miRNAs (miR-1252, miR-433, miR-553, miR-138-5p and miR-2053) are significantly differentially expressed in pre-manifest gene-positive HD cases vs. gene-negative controls. We also explored the miRNAs associated with HD severity by correlating the miRNA expression with CAP scores of 115 pre-manifest HD samples and found that 41 and 24 miRNAs are negatively and positively correlated with CAP scores significantly. Furthermore, target gene set of miR-138 and miR-433 , its co-expressed mRNAs in ROSMAP, and differentially expressed mRNAs of HD reveal four overlap genes (CASP7, CNOT6L, TMED and FERMT2). In summary, our study provides new insights into biomarker of Huntington’s disease by analyzing the cross-sectional miRNA expression data in blood.

overall_design: In this study, total RNAs for 136 CSF samples, incl. 21 controls and 115 HD, were requested from PREDICT-HD consortium. We then sequenced the miRNA using Illumina TruSeq kit. After mapping and quantifying the miRNA normalized expression level, we called differential expressed miRNAs between control and HD using SVA, after ajusting the covariates.

first: Zhuo

last: Wang

first: Clemens

last: Scherzer


title: Differential expression analysis of miRNAs expressed in blood and CSF of Huntington's disease

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


title: Pancreatic cancer-derived exosomes induce apoptosis of T lymphocytes through the p38 MAPK signal transduction pathway

city: Hangzhou

first: Tao

last: Shen

address: 866 Yuhangtang Rd

institute: Zhejiang University

summary: Pancreatic cancer is the fourth most lethal malignancy, which is characterized by poor immunogenicity. Pancreatic cancer cells take various strategies to suppress host immune response, evade immune defenses, and facilitate tumor growth and development. As a mode of long-range intercellular communication, cancer-derived exosomes contribute to the impairment of the immune system. However, the mechanisms that induce changes in the activities of signal transduction pathways in immune cells, which are influenced by tumor-derived exosomes, are poorly understood. We treated peripheral T lymphocytes with pancreatic cancer-derived exosomes, performed RNA-seq and Gene Set Enrichment Analysis to explore the pivotal signaling pathway that mediates apoptosis in exosomes-treated T lymphocytes.

overall_design: T lymphoblasts were obtained from three donors and total RNA was isolated from cells  with exosomes treated (Exo-T) or with PBS treated (Ctrl-T).

first: Shengnan

last: Jia

first: Chengfei

last: Shi

first: Senhao

last: Zhou

first: Xiaofan

last: Pu

first: Zhengrong

last: Wu

first: Guoping

last: Ding

first: Liping

last: Cao


title: Transcriptome-wide analysis of RNA binding and splicing alterations induced by SRSF2 P95 mutations in myelodysplasia

city: New Haven, US & Trento, Italy

first: Toma

last: Tebaldi

state: CT

address: 300 George Street

department: CIBIO & Department of Internal Medicine, Yale Cancer Center

institute: Yale University & University of Trento

summary:
Mutations in the splicing factor Serine Arginine Rich Splicing Factor 2 (SRSF2) occur in over 30% of patients with myelodysplasia (MDS) and a subset of patients with acute myeloid leukemia (AML) and portend a poor prognosis. SRSF2 is ubiquitously expressed and directs exon inclusion or exclusion in a sequence and context dependent manner. SRSF2 mutations almost exclusively affect the proline at position 95 in the C-terminus of the RNA binding domain.  We here show how a mutation in SRSF2 (P95H) affects its normal function in vivo on a transcriptome-wide basis via RNA crosslinking and immunoprecipitation (HITS-CLIP) and parallel quantification of transcript levels (RNA-seq), leading to the identification of differentially bound and alternatively spliced SRSF2 targets.
Keywords: Splicing, myeloid neoplasia, SRSF2, HITS-CLIP

overall_design: In this study, we performed high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP) to determine the function of mutant SRSF2 in the context of a human hematopoietic cell line. Human erythroid leukemia (HEL) cell lines were stably transduced with either wild type SRSF2 (WT) or mutant SRSF2 (P95H, MUT). HITS-CLIP was performed in biological quadruplicate. RNA-seq was performed in biological duplicate.

first: Yang

last: Liang

first: Kai

last: Rejeski

first: Poorval

last: Joshi

first: Giovanni

last: Stefani

first: Stephanie

last: Halene


title: JDP2 - an Oncogenic bZIP Transcription Factor in T-cell Acute Lymphoblastic Leukemia [ChIP-Seq]

city: Cambridge

first: Richard

last: Young

address: 9 Cambridge Center

institute: Whitehead Institute for Biomedical Research

summary: A substantial subset of patients with T-cell acute lymphoblastic leukemia (T-ALL) develops resistance to steroids and succumb to their disease. JDP2 encodes a bZIP protein that has been implicated as a T-ALL oncogene from insertional mutagenesis studies in mice, but its role in human T-ALL pathogenesis has remained obscure. Here we show JDP2 is aberrantly expressed in a subset of T-ALL patients and is associated with poor survival. JDP2 is required for T-ALL cell survival, as its depletion by shRNA knockdown leads to apoptosis. Mechanistically, JDP2 regulates pro-survival signaling through direct transcriptional regulation of MCL1. Furthermore, JDP2 is one of few oncogenes capable of initiating T-ALL in transgenic zebrafish. Notably, thymocytes from rag2:jdp2 transgenic zebrafish express high levels of mcl1, and demonstrate resistance to steroids in vivo. These studies establish JDP2 as a novel oncogene in high-risk T-ALL, and implicate overexpression of MCL1 as a mechanism of steroid resistance in JDP2-overexpressing cells.

overall_design: ChIP-Seq targeting JDP2 in Loucy T-ALL cells

first: Marc

last: Mansour

first: Shuning

last: He

first: Zhaodong

last: Li

first: Riadh

last: Lobbardi

first: Brian

last: Abraham

last: Hug

first: Sunniyat

last: Rahman

first: Theresa

middle: E

last: Leon

first: You-Yi

last: Kuang

first: Mark

middle: W

last: Zimmerman

first: Traci

last: Blonquist

first: Evisa

last: Gjini

first: Alejandro

last: Gutierrez

first: Qin

last: Tang

first: Laura

last: Garcia-Perez

first: Karin

last: Pike-Overzet

first: Lars

last: Anders

first: Alla

last: Berezovskaya

first: Yi

first: Leonard

middle: I

last: Zon

first: Donna

last: Neuberg

first: Adele

last: Fielding

first: Frank

last: Staal

first: David

last: Langenau

first: Takaomi

last: Sanda

first: A

last: Look


title: JDP2 - an Oncogenic bZIP Transcription Factor in T-cell Acute Lymphoblastic Leukemia [RNA-Seq]

first: Richard

last: Young

overall_design: RNA-seq in T-ALL cells with and without short hairpins against JDP2

first: Marc

last: Mansour

first: Shuning

last: He

first: Zhaodong

last: Li

first: Riadh

last: Lobbardi

first: Brian

last: Abraham

first: Clemens

last: Hug

first: Sunniyat

last: Rahman

first: Theresa

last: Leon

first: You-Yi

last: Kuang

first: Mark

last: Zhou


title: Transcriptional plasticity, priming and commitment in hematopoietic lineages [RNA-seq]

first: Ido

last: Amit

summary: Differentiation of adult hematopoietic stem cells (HSC) constantly produces the cell types of the blood and immune system. The dynamics of this process and the hierarchy of downstream oligopotent stem cell differentiation remain controversial. Here we dissect hematopoietic progenitor populations in a minimally biased fashion using extensive single cell sampling from murine bone marrow. We characterize the HSC population, define its quiescent transcriptional program and validate it with label retaining assays and cytokine mediated stimulations. Analysis of initial HSC commitment defines marked bifurcation of erythroid/megakaryocytic cells from myeloid/lymphoid lineages. Unexpectedly, we find states that mix transcription of pre-myeloid and pre-lymphoid genes. This suggests a model in which more than one differentiation trajectory can link HSC to several cell types. Dendritic cells are thus linked with both monocyte and lymphocyte precursors. Our data support a model of hematopoiesis balancing relaxation of an HSC quiescent state, gradual bifurcations and trans-differentiation.

overall_design:
Bone marrow hematopoietic progenitors mRNA profiles from single cells were generated by deep sequencing of thousands of single cells, sequenced in several batches on an Illumina NextSeq
Experiment was paired-end, but read2 was used to read cell and molecule barcodes only.
Additional details about experimental design (associating each single cell with its amplification batch and index sorting readout) available as Series supplementary file.

first: Amos

last: Tanay

first: Amir

last: Giladi

first: Franziska

last: Paul


title: JDP2 - an Oncogenic bZIP Transcription Factor in T-cell Acute Lymphoblastic Leukemia

overall_design: Refer to individual Series


title: A novel systems immunology approach identifies the collective impact of five miRNAs in Th2 inflammation (mRNA)

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

institute: Aalborg University

summary: Allergic asthma is a chronic inflammatory disease dominated by a CD4+ T helper 2 (Th2) cell signature. The immune response amplifies in self-enforcing loops, promoting Th2-driven cellular immunity and leaving the host unable to terminate inflammation. Posttranscriptional mechanisms, including miRNAs, are pivotal in maintaining immune-homeostasis. Since an altered expression of various miRNAs has been associated with T cell-driven diseases, including asthma, we hypothesized that miRNAs control mechanisms ensuring Th2 stability and maintenance in the lung. We isolated murine CD4+ Th2 cells from allergic inflamed lungs and profiled gene and microRNA expression.

overall_design: Tissue resident Th2 cells were isolated  at two stages of Ovalbumin-induced allergic airway inflammation from lung tissue for RNA extraction and hybridization on Affymetrix microarrays. We obtained live cells by fluorescent-activated cells sorting based on surface marker expression at different stages:  antigen-naive CD4+ T cells from spleens of sham-treated mice, Th2 cells after polarization and recruitment to the inflamed tissue (early Th2), and cells from chronic inflamed tissue (stable Th2). We sought to decipher mechanisms regulating the persistence of chronic allergic inflammation.

first: S

last: Kılıç


title: A novel systems immunology approach identifies the collective impact of five miRNAs in Th2 inflammation

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

platform_organism:
Mus musculus
synthetic construct


title: Temporal profiling of redox-dependent heterogeneity in single cells

status: Public on Jun 17 2018

city: Jerusalem

first: Nir

last: Friedman

address: Givat Ram

institute: The Hebrew University of Jerusalem

summary: The cellular redox status plays an essential role in diverse cellular functions,  including proliferation, protein homeostasis, and aging. Thus even cells with  identical genetic background but different redox status behave differently. Here,  we propose a non-laborious and robust methodology to quantify cell-to- cell  redox-dependent variability within thousands of cells, detect oxidation levels in  cytosol, mitochondria, and peroxisome, and sort cells based on their redox  status.  We report that cells of the same age have a bi-modular distribution of reduced  and oxidized cells starting in the late logarithmic phase. Although the ratio  between the oxidized and reduced subpopulations changes during chronological  aging, their growth, proteomic and transcriptomic features are conserved during  their first days of chronological aging. A comparative proteomic analysis  identified three key proteins, Hsp30, Dhh1, and Pnc1, which affect basal  oxidation levels and may serve as first line of defense proteins in redox  homeostasis.

overall_design: The dataset includes 12 3'RNA-Seq samples.


title: Genes expression of SU-DHL-2 cells treated with IL-17A

status: Public on Jun 16 2018

city: Guangzhou

first: Weijie

last: Zhong

address: Panfu road 1st

institute: Guangzhou First People's Hospital

summary: To further figure out the molecular mechanisms of IL-17A-mediated DLBCL cells growth, we used the Whole Human Genome Oligo Microarray (4×44K, Agilent Technologies)  to identify genes expression. Six samples of SU-DHL-2 cells (2×10^6 cells/ml) co-cultured with or without IL-17A (200pg/ml) for 72hr in vivo. Three samples of SU-DHL-2 cells were all co-cultured with IL-17A , other three samples of SU-DHL-2 cells without IL-17A treatment were used as controls. Then, all these six samples of SU-DHL-2 cells were measured by microarray.

first: Qingshan


title: Mutations in the SWI/SNF chromatin remodeling complex induce metabolic rewiring and dependence on oxidative phosphorylation

city: Houston

first: Kunal

last: Rai

state: TX

address: 1801 East Rd

department: Genomic Medicine

institute: MD Anderson Cancer Center

summary: Lung cancer is a devastating disease that remains the top cause of cancer mortality. While targeted therapies against EGFR and EML4-ALK fusion and recent advances in immunotherapy have shown substantial clinical benefit for some patients, the vast majority of patients with lung cancer still lack effective therapies underscoring the dire need for more context-specific therapeutics. Cancer genomic studies have identified frequent genetic alterations in chromatin and epigenetic regulators including inactivating mutations in components of the SWI/SNF chromatin remodeling complex. In lung adenocarcinoma, about 20% of tumors have inactivating mutations in components of the SWI/SNF chromatin remodeling complex including SMARCA4 and ARID1A. With the aim of understanding the mechanism of tumor development driven by mutations in this complex, we developed a genetically engineered mouse (GEM) model of lung adenocarcinoma by selectively ablating Smarca4 in the lung epithelium. We demonstrate that Smarca4 acts as a bona fide tumor suppressor and cooperates with p53 loss and Kras activation. Cross species integrative gene expression analyses revealed signature of enhanced oxidative phosphorylation (OXPHOS) in SMARCA4 mutant murine as well as human lung adenocarcinomas. We further show that SMARCA4 mutant cells have increased oxygen consumption and increased respiratory capacity primarily driven by increased expression of the mitochondrial master regulator, PGC1-α. Importantly, we show that SMARCA4 and other SWI/SNF mutant lung cancer cell lines and xenograft tumors have exquisite sensitivity to inhibition of OXPHOS by a novel small molecule, IACS-010759, that is under clinical development. Mechanistically, we show that SMARCA4 deficient cells have a blunted transcriptional response to energy stress creating a therapeutically attractive collateral vulnerability. These findings provide the mechanistic basis for further development of OXPHOS inhibitors as therapeutics against SWI/SNF mutant tumors.

overall_design: Examination of genomic localization of SMARCA4 in H1299 cells stably transduced with an inducible SMARCA4 vector upon doxycycline adminstration to induce expression of SMARCA4.

first: Yonathan

last: Deribe

first: Andrew

last: Futreal

first: Christopher

last: Terranova


title: Pancreatic Islet-Autonomous Signals Modulate Identity Changes of Glucagon+ α-Cells

city: Indianapolis

first: Simone

last: Gupta

address: Lilly Corporate Center

institute: Eli Lilly & Company

summary: The mechanisms restricting regeneration and maintaining cell identity upon injury are poorly characterized in higher vertebrates. Upon β-cell loss, 1-2% of the glucagon-producing α-cells spontaneously engage insulin production in mice. Here we explore the mechanisms of this plasticity. We show that the adaptive α-cell identity changes are constrained by intra-islet Insulin- and Smoothened-mediated signaling, among others. Combining β-cell loss, or insulin signaling inhibition, with Smoothened inactivation in α- or δ-cells, stimulates insulin production in more α-cells. These findings suggest that removing constitutive “brake signals” is crucial for neutralizing the refractoriness to adaptive cell-fate changes. It appears that cell identity maintenance is an active process mediated by repressive signals curbing an intrinsic trend of differentiated cells to change.

overall_design: RNA-Seq analyses on five purified cells namely, mature α-cells, mature β-cells, α-cells 30 days after DT, α-cells ectopically expressing PDX1 and α-cells expressing PDX1

first: Valentina

last: Cigliola

first: Luiza

last: Ghila

first: Fabrizio

last: Thorel

first: Takeshi

last: Miyatsuka

first: Hideaki

last: Kaneto

last: Wright

last: Magnuson

first: Anna

middle: B

last: Osipovich

first: Maike

last: Sander

first: Delphine

last: Baronnier

first: Kenichiro

last: Furuyama

first: Melissa

last: Thomas

first: Simona

last: Chera

first: Pedro

last: Herrera


title: Transcriptional analysis of adipose tissue during post-natal development reveals depot-specific responsiveness to maternal dietary supplementation

status: Public on Jun 15 2018

city: Nottingham

first: Hernan

middle: Pablo

last: Fainberg

address: Derby Rd

department: Division of Child Health, Obstetrics & Gynaecology

institute: The University of Nottingham

summary:
In this study we use ovis aries as a comparative model
The objective of the study was to compared changes in genetic interactions in five adipose tissue deposits during early development.

overall_design: In order to identify changes in gene regulation with age, we performed a transcriptomic comparison between all 5 depots at 7 and 28 days of age. Thus, we determined the global  changes gene expression signatures on Omental (OM), Perirenal (PrR), Epicardial (EpC), Subcutaneuos (Su) and Sternal (St) fat. To gain insight into how may change with age the gene expression in these fat depots, we identified functional modules of co-expressed genes using several different bioinformatics approaches, including WGCNA and gene ontology analysis.

first: H

first: R

last: Alagal

first: M

last: Birtwistle

first: A

last: Alhaddad

last: Pope

first: G

last: Davies

last: Woods

last: Castellanos

first: S

last: May

first: C

last: Ortori

first: D

last: Barrett

first: V

last: Perry

first: F

last: Wiens

first: B

last: Stahl

first: E

last: van der Beek

last: Sacks

last: Budge

last: Symonds


title: Integrative single-cell analysis reveals human germinal center dynamics de-synchronized in B cell lymphoma

city: Marseille

first: Pierre

last: Milpied

address: 163 avenue de Luminy

institute: CIML - Centre d'Immunologie de Marseille-Luminy (U1104)

summary: Most adult B cell  lymphomas originate from germinal center (GC) B cells but it is unclear to what extent overt lymphoma B cells retain GC B cell functional dynamics or are blocked in a particular stage of the GC reaction. Here, we used integrative single-cell analysis of phenotype, gene expression and IGH sequence to track the characteristic human GC B cell program in follicular lymphoma (FL) B cells. By modeling the cyclic continuum of GC B cell transitional states, we identified characteristic patterns of synchronously expressed gene clusters. GC-specific gene expression synchrony was lost in single lymphoma B cells. Yet, distinct FL-specific cell states co-existed within single patient biopsies. Our data show that lymphoma B cells are not blocked in a GC B cell state but may adopt new dynamic modes of functional diversity, opening novel definitions of lymphoma identity.

overall_design: First sample: Frozen live cell suspensions of normal B-cells (CD3-FITC, CD14-FITC, IgD-FITC, CD56-V450, CD20-PE-Cy7, CD38-BV785, CD10-PE) mixed with mouse cells. Second sample: Frozen live cell suspensions of human follicular lymphoma mixed with mouse cells.

first: Inaki

last: Cervera-Marzal


title: The ESCRT-III protein CHMP1A mediates secretion of sonic hedgehog on a novel class of extracellular vesicles

city: Santa Cruz

first: Ali

last: Shariati

address: 1156 High St

department: Biomolecular Engineering

institute: University of California Santa Cruz

summary: Extracellular vesicles (EVs) enable cell-to-cell communication in the nervous system essential for development and adult function. Endosomal Sorting Complex Required for Transport (ESCRT) complex proteins regulate EV formation and release. Recent work shows loss of function (LOF) mutations in, CHMP1A, which encodes one ESCRT-III member, cause autosomal recessive microcephaly with pontocerebellar hypoplasia in humans (Mochida et al., 2012). Here we show CHMP1A is required for maintenance of progenitors in human cerebral organoids and that mouse Chmp1a is required for progenitor proliferation in cortex and cerebellum and specifically for sonic hedgehog (SHH) mediated proliferation through SHH secretion. CHMP1A mutation reduces intraluminal vesicle (ILV) formation in multivesicular bodies (MVBs), and EV release. SHH protein is present on a subset of EVs marked by a unique set of proteins we call ART-EVs. CHMP1A’s requirement in formation of ART-EVs and other EVs provides a model to elucidate EV functions in multiple brain processes.

overall_design: Gene expression profiling in a hiPSC WT line and a hiPSC CHMP1A null line. Comparative analysis by RNA-seq in hIPSCs and directed differentiation to cerebral organoids. Treatment with smoothened agonist (SAG) was used for examination of SHH dependent response in WT and CHMP1A null organoids.

first: Michael

last: Coulter

first: Cristina

last: Dorobantu

first: Gerrald

middle: A

last: Lodewijk

first: François

last: Delalande

first: Sarah

last: Cianferani

first: Vijay

last: Ganesh

first: Richard

last: Smith

first: Elaine

last: Lim

last: Xu

first: Song

last: Pang

first: Eric

last: Wong

first: Hart

middle: G

last: Lidov

first: Monica

last: Calicchio

first: Edward

last: Yang

first: Dilenny

middle: M

last: Gonzalez

first: Thorsten

last: Schlaeger

first: Ganesh

last: Mochida

first: Harald

last: Hess

first: Wei-Chung

last: Lee

first: Maria

last: Lehtinen

first: Tomas

last: Kirchhausen

first: David

last: Haussler

first: Frank

last: Jacobs

first: Raphael

last: Gaudin

first: Christopher

last: Walsh


title: Distinct Gene Expression Profiles Define Anaplastic Grade in Retinoblastoma

city: Atlanta

first: Hans

last: Grossniklaus

state: Georgia

address: 1365 Clifton Rd

institute: Emory Eye Center

summary:
Morbidity and mortality associated with retinoblastoma have decreased drastically in recent decades, in large part due to better prediction of high-risk disease and appropriate treatment stratification. High-risk histopathologic features and severe anaplasia both predict the need for more aggressive treatment; however, not all centers are able to easily assess tumor samples for degree of anaplasia. Instead, identification of genetic signatures able to distinguish among anaplastic grades and thus predict high versus low risk retinoblastoma would facilitate appropriate risk stratification in a wider patient population. A better understanding of genes dysregulated in anaplasia would also yield valuable insights into pathways underlying the development of more severe retinoblastoma. Here, we present the histopathologic and gene expression analysis of 28 retinoblastoma cases using microarray analysis. Tumors of differing anaplastic grade show clear differential gene expression, with significant dysregulation of unique genes and pathways in severe anaplasia. Photoreceptor and nucleoporin expression in particular are identified as highly dysregulated in severe anaplasia and suggest particular cellular processes contributing to the development of increased retinoblastoma severity. A limited set of highly differentially expressed genes are also able to accurately predict severe anaplasia in our dataset. Together, these data contribute to the understanding of the development of anaplasia and facilitate the identification of genetic markers of high-risk retinoblastoma.
We used microarray analysis to determine the gene expression patterns of 28 human retinoblastoma samples according to their grade of cellular anaplasia.

overall_design: The anaplastic grade of 28 retinoblastoma cases was determined. Total RNA was extracted from the 28 retinoblastoma samples in addition to 3 matched retinocytoma samples and 3 matched normal retina samples and analyzed using Affymetrix arrays.

first: Lauren

last: Hudson

first: Pia

last: Mendoza

first: William

first: Alison

last: Ziesel

first: G

last: Hubbard

first: Jill

last: Wells

first: Bhakti

last: Dwivedi

first: Jeanne

last: Kowalski

first: Sandra

last: Seby

first: Viren

last: Patel

first: Eldon

last: Geisert

first: Charles

last: Specht


title: Human intestinal biopsy gene expression after infection with Salmonella enterica serovar Typhi

first: Alessio

last: Fasano

address: 114 16th Street

institute: Massachusetts General Hospital

summary: This study describes how Salmonella Typhi, the pathogen responsible for typhoid fever, uses similar strategies to escape immune defense responses and survive within its human host. To elucidate the early mechanisms of typhoid fever, we performed studies using healthy human intestinal tissue samples to analyze gene expression changes in human intestinal specimens and bacterial cells both separately and after colonization. Our results showed mechanistic strategies that S. Typhi uses to rearrange the cellular machinery of the host cytoskeleton to successfully invade the intestinal epithelium, promote polarized cytokine release and evade immune system activation by downregulating genes involved in antigen sampling and presentation during infection.

sample_organism: Salmonella enterica subsp. enterica serovar Typhi str. Ty2

overall_design: mRNA was collected from four control biopsies, five infected biopsies and four control bacterial samples. RNA sequencing was done using 1x50bp SR, HiSeq 2500; rapid run flow cells and analyzed using an Ergatis-based RNA-Seq analysis pipeline.

first: Kourtney

middle: P

last: Nickerson


title: Comparison of transcriptional responses to sulfur mustard, nitrogen mustard, and half mustard exposure in epidermal keratinocytes

city: Aberdeen Proving Ground

first: James

middle: F

last: Dillman

state: MD

address: 3100 Ricketts Point Rd

department: Cell and Molecular Biology Branch

institute: U.S. Army Medical Research Institute of Chemical Defense

summary: Sulfur mustard (SM) is a potent vesicant that targets epithelial cells and tissues. Most vesicant research has been performed using bona fide SM; however, some studies have used simulants, most notably half mustard (2-chloroethyl ethylsulfide; CEES) and nitrogen mustard (mechlorethamine; NM). Although CEES and NM have similarities to SM and can cause vesication, there are distinct differences in the chemical structures and physical properties of these compounds that may impact their toxic effects. Microarray analysis of cultured primary human epidermal keratinocytes (HEK) exposed to each of these vesicants was performed to directly compare the transcriptional responses induced by these vesicants. HEK were exposed in triplicate to concentrations ranging from 0-1000 µM for SM and NM and 0-4000 µM for CEES. Cells were harvested at 1, 2, 4, 8, 16, and 24 h and the RNA isolated for microarray analysis. Transcriptional responses were phenotypically anchored to cell morphology. The dataset was filtered by exposure and timepoint, and an analysis of variance was performed using dose as the factor. The top 500 genes ranked by p-value were analyzed using gene ontology algorithms to identify biological pathways significantly affected by each vesicant. At 2 h post-exposure, p53 signaling, Erk/MAPK signaling, and BMP signaling were significantly affected by all three vesicants. At 4 h post-exposure, p53 signaling , B cell activating factor, and glucocorticoid receptor signaling were significantly affected by all three vesicants. At 8 h post-exposure, there were no significant pathways commonly affected by all three vesicants. These results suggest that, although there are similarities in the transcriptional responses to each of these vesicants, the transcriptional responses appear to differ over time. Thus, extrapolation of results obtained with one vesicant to other vesicants may be complex and may have important implications for the development of vesicant therapeutics.

overall_design: For sulfur mustard (Bis-[2-chloroethyl] sulfide) or nitrogen mustard (mechlorethamine hydrochloride), NHEK were exposed to 12.5 µM, 25 µM, 50 µM, 100 µM, 200 µM, 400 µM, 600 µM, 800 µM, or 1000 µM.  For half mustard (2-chloroethyl ethyl sulfide), NHEK were exposed to 100 µM, 500 µM, 1000 µM, 1500 µM, 2000 µM, 2500 µM, 3000 µM, 3500 µM or 4000 µM.  After exposure, cells were incubated in a chemical surety fume hood for one hour at 37◦C with ambient air, and then placed at 37◦C with 5% CO2 for the remainder of the exposure period.  Exposure periods were 1h, 2h, 4h, 8h, 16h, and 24h.  Time matched controls, which received an equivalent volume of fresh KGM were carried out with each exposure group. n=3 for all experimental groups.

last: Phillips

first: Cristin

middle: C

last: Rothwell


title: Inflammatory Response and Host-Donor Chimerism Defined by Single Cell RNA-Seq of Allograft Biopsy

city: St. Louis

first: Haojia

last: Wu

address: 600 S Euclid Ave

institute: Washington University in St. Louis

summary: Kidney transplantation offers the best survival and quality of life for patients’ with end-stage kidney disease. The major barrier to successful long-term transplantation is the host’s immune response to alloantigens’ causing rejection of the transplant. The complexity of this immune response in kidney transplantation is still not fully understood and effective treatment strategies are needed. To better understand rejection at the molecular and cellular level we characterized 4,487 cells from a single biopsy core from a kidney transplant undergoing mixed rejection using single cell RNA sequencing.

overall_design: InDrop was used to generate single cell profiles from a allograft kidney biopsy

first: Benjamin

middle: D

last: Humphreys


title: Developmental vascular regression is regulated by a Wnt/b-catenin, MYC, P21 (CDKN1A) pathway that controls cell proliferation and cell death

city: Cincinnati

first: Gowri

last: Nayak Sarangdhar

state: Ohio

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: Normal development requires tight regulation of cell proliferation and cell death. Here, we investigated these control mechanisms in the hyaloid vessels, a temporary vascular network in the mammalian eye that requires a Wnt/β-catenin response for scheduled regression. Transcriptome analysis of the postnatal day 5 mouse hyaloid showed expression of several Wnt pathway proteins. We investigated whether the hyaloid Wnt response was linked to the oncogene Myc, and the cyclin-dependent kinase inhibitor P21 (CDKN1A), both established regulators of cell cycle progression and cell death. Our analysis showed that the Wnt pathway coreceptors LRP5 and LRP6 have overlapping activities mediating the Wnt/β-catenin signaling in hyaloid vascular endothelial cells (VECs). We also showed that both Myc and Cdkn1a are downstream of the Wnt response and are required for hyaloid regression but for different reasons. Conditional deletion of Myc in VECs suppressed both proliferation and cell death. By contrast, conditional deletion of Cdkn1a resulted in VEC over-proliferation that countered the effects of cell death on regression. When combined with analysis of MYC, and P21 protein levels, this analysis suggests that a Wnt/β-catenin, MYC-P21 pathway regulates scheduled hyaloid vessel regression.

overall_design: Hyaloid vascular preparations from postnatal day 5 mice were harvested in cold PBS and RNA extracted in Tri Reagent. RNA amplifcation was performed on total RNA before cDNA library was made. Samples were then sequenced using Illimina HiSeq2500 to obtain 25-30 million paired-end reads.

last: Nayak

first: Yoshinobu

last: Odaka

first: Vikram

last: Prasad

first: Alyssa

last: Solano

first: Eun-Jin

last: Yeo

first: Shruti

last: Vemaraju

first: Jeffery

last: Molkentin

first: Andreas

last: Trumpp

first: Bart

last: Williams

first: Sujata

last: Rao

first: Richard

last: Lang


title: Analysis of MAP Kinase Signaling Molecules p38, JNK, and Erk in Sulfur Mustard Toxicity Using Pharmacological Inhibitors and Gene Expression Profiling

last: Dillman

summary: Bis-2-chloroethyl sulfide (sulfur mustard, SM) is a potent alkylating agent and vesicant.  Exposure to SM results in activation of numerous signaling cascades, including mitogen-activated protein kinase (MAPK) signaling pathways.  These pathways include the Erk, p38, and JNK pathways, which are involved in cell growth, inflammation, and stress signaling.  However, the precise roles of these pathways in SM toxicity have not been fully elucidated.  We used Western blotting and microarray analysis to examine the activation and role of each pathway following SM exposure in primary human epidermal keratinocytes.  Western blotting revealed increased phosphorylation of p38 and JNK following SM exposure; however, phosphorylation of Erk was equivocal, suggesting that growth conditions may impact activation of Erk by SM.  We used pharmacologic inhibitors to target each MAPK and then compared the gene expression profiles to identify SM-induced gene networks regulated by each MAPK.  Cells were pretreated with 10 µM SB 203580 (p38 inhibitor), PD 98059 (Erk inhibitor), or SP 600125 (JNK inhibitor) 60 minutes before exposure to 200 µM SM.  Cells were harvested at 1h, 4h, and 8h post-exposure, and RNA was extracted for synthesis of microarray probes.  Probes were hybridized to Affymetrix U133 Plus 2.0 arrays for gene expression profiling.  Analysis of variance was performed to identify genes significantly modulated due to pharmacologic inhibition in SM-exposed cells.  Pathway mapping confirmed alterations in SM-induced Erk, JNK, and p38 MAPK signaling due to pharmacologic inhibition.  SM-induced expression of IL-8, IL-6, and TNF-alpha was decreased by p38 MAPK inhibition, but not by inhibition of other MAPKs.  Based on the number of significant pathways mapped to each MAPK in the presence and absence of inhibitors, the p38 MAPK pathway appeared to be the MAPK pathway most responsive to SM exposure.  Interestingly, pathway mapping of the microarray data identified potential cross-talk between MAPK signaling pathways and other pathways involved in SM-induced signaling.  Mining of these results will increase our understanding of the role of MAPK pathways in SM-induced signal transduction and may identify potential therapeutic targets for medical countermeasure development.

overall_design: Cultured cells were treated with one of three pharmacological inhibitors and exposed to 0 micromolar or 200 micromolar sulfur mustard and collected at 1h, 4h, or 8h post exposure.  Three replicates (n=3) were collected for each experimental group.

first: Chelsea

last: Crum

first: Patrick

last: Everley


title: Nfkbid represents an Idd7 locus gene contributing to impaired thymic deletion of CD8 T-cells in NOD mice

status: Public on Jun 14 2018

city: Bar Harbor

first: Timothy

middle: Michael

last: Stearns

state: ME

address: 600 Main Street

department: Computational Sciences

institute: The Jackson Laboratory

summary:
In both NOD mice and humans, the development of type 1 diabetes (T1D) is dependent in part on autoreactive CD8+ T-cells recognizing pancreatic ß-cell peptides presented by often quite common MHC class I variants.  Studies in NOD mice previously revealed the common H2-Kd and/or H2-Db class I molecules expressed by this strain acquire an aberrant ability to mediate pathogenic CD8 T-cell responses through interactions with T1D susceptibility (Idd) genes outside the MHC.   A gene(s) mapping to the Idd7 locus on proximal Chromosome 7 was previously shown to be an important contributor to the failure of the common class I molecules expressed by NOD mice to mediate the normal thymic negative selection of diabetogenic CD8+ T-cells. Using an inducible model of thymic negative selection and mRNA transcript analyses we initially identified an elevated Nfkbid expression variant as a strong candidate for an NOD Idd7 region gene contributing to impaired thymic deletion of diabetogenic CD8+ T-cells. CRISPR/Cas9-mediated genetic attenuation of Nfkbid expression in NOD mice resulted in improved negative selection of autoreactive diabetogenic AI4 and NY8.3 CD8+ T-cells. These results indicated allelic variants of Nfkbid represent an Idd7 gene contributing to the efficiency of intrathymic deletion of diabetogenic CD8+ T-cells.  However, while enhancing thymic deletion of pathogenic CD8+ T-cells, ablation of Nfkbid expression surprisingly accelerated T1D onset in NOD mice likely by numerically decreasing regulatory T- and B-lymphocytes (Tregs/Bregs), thereby reducing their peripheral immunosuppressive effects.
We used microarray analysis to identify differentialy expressed genes in thymus under conditions of induced thymic negative selection. We compare two mice strains, NOD-LCMV vs NOD.Ln82-LCMV (a congenic stock for a C57BL/6 derived segment delimited by markers D7Mit117–D7Mit247).

overall_design: Three to five 5-week-old, NOD.LCMV and NOD.Ln82-LCMV female mice were i.v. injected with 0.5μg of gp33 (KAVYNFATM) or Db binding control peptide (ASNENMETM). Two hours post-injection, whole thymus tissue was processed for total RNA extraction. RNA samples were hybridized to Affymetrix Mouse Gene 1.0 ST Arrays. A total of 15 samples were analyzed. 3-5 biological replicates by experimental group.

first: Maximiliano

last: Presa

first: Jeremy

middle: J

last: Racine

first: Jennifer

middle: R

last: Dwyer

first: Deanna

last: Lamont

last: Ratiu

first: Vishal

last: Kumar Sarsani

first: Yi-Guang

last: Chen

first: Aron

last: Geurts

first: Ingo

last: Schmitz

last: Allocco

first: Harold

last: Chapman

first: David

middle: V

last: Serreze


title: Gene Expression Profile Comparison of Human Epidermal Keratinocyte Cell Culture Models Following Sulfur Mustard Exposure

first: James

summary: Normal human epidermal keratinocytes (NHEKs) and HaCaTs have been widely used as cell culture models to study the effects of cutaneous sulfur mustard (HD) exposure.  While these cell lines are similar, one key difference is that NHEKs are primary cells, whereas HaCaT cells are a transformed line with a mutation in the p53 gene.  However, the impact of this mutation on the response of HaCaT cells to HD is unclear.  Thus, gene expression profiling was performed to compare the transcriptional responses of NHEKs and HaCaTs after HD exposure.  Cells were exposed to 0, 25, and 200 µM HD, harvested at 1 h and 8 h post-exposure, and processed for microarray analysis.   Principal component analysis of the microarray data suggested profile differences based on cell type, but both cell types respond similarly to HD with regard to dose and time.   To further analyze the expression profiles at various doses, the dataset was filtered by dose, and an analysis of variance was performed using cell type as the factor; the pathways most significantly different between these cell types were identified.   At all three doses, the p53 and N-glycan degradation pathways were significantly different between NHEKs and HaCaTs.   Interestingly, p53 responsive genes showed differences and similarities across cell types, which may provide insight into the role of p53 in HD toxicity. The inflammatory pathways expected to respond to HD exposure were not significantly different between cell types, suggesting that both NHEKs and HaCaTs are appropriate models to study the inflammatory effects of HD.

overall_design: Cells were exposed to 0 µM, 25 µM, or 200 µM sulfur mustard and collected at 1 h or 8 h post exposure. Time matched controls were included for each group.  Three replicates (n=3) were collected for each experimental group.

first: Cristin

last: Rothwell


title: Role of GATA in DN3 stage thymocytes

city: Ann Arbor

first: Tomonori

last: Hosoya

address: 109 Zina Pitcher Place

department: CDB

institute: University of Michigan

summary: RNA-seq in DN3 stage thymocytes isolated from wild type and Gata3 hypomorphic mutant mouse

overall_design: Donor fetal liver cells were injected into irradiated recipient mouse.  16 weeks after donor cell injection, DN3 stage thymocytes were sorted, and then analyzed by RNA-seq.

last: Engel


title: GATA3 abundance is a critical determinant of T cell receptor beta allelic exclusion [GATA3-GFP]

summary: RNA-seq in GFP-positive and GFP-negative DN4 stage thymocytes isolated from GATA3-GFP fusion protein knock-in mouse

overall_design: GFP-positive and GFP-negative DN4 stage thymocytes were isolated from adult mouse, and then analyzed by RNA-seq

first: Chia-Jui

last: Ku

first: Tomonoti