title: Adenoviral Vector Transduction of Dendritic Cells is Inhibited by Plasma from Cancer Patients

city: BETHESDA

first: PING

last: JIN

state: MD

address: 9000 ROCKVILLE PIKE

department: DTM

institute: CC/DTM/NIH

summary: Background: Pooled AB serum is often used as a media supplement for cell culture but it has the potential to transmit infectious diseases. To avoid this risk, we used autologous plasma as a media supplement for manufacturing dendritic cells (DCs) for cancer immunotherapy.  We noticed inconsistences in the DCs and investigated its nature and cause.   Methods:  adHER2/neu DCs for 21 patients were manufactured from autologous peripheral blood monocytes which were treated with G-CSF and IL-4 for 3 days, transduced with Ad5f35HER2ECTM and then treated with lipopolysaccharide and IFN- for one day. The cells were cultured in RPMI-1640 supplemented with either 10% heat inactivated autologous or AB plasma.   Results: Twenty-eight adHER2/neu DCs were manufactured for 21 patients using autologous plasma and 68 were manufactured for 20 of those patients using AB plasma. The expression of HER2/neu was less for DCs manufactured with autologous plasma (70.3±33.3% vs 86.1±22.8%, p<0.01). Manufacturing adHER2/neu DCs using monocytes from 3 healthy subjects and plasma from one patient with low HER2/neu expression (18%) resulted in low HER2/neu expression by all three DCs (13%, 16% and 23%).  Analysis of the levels of 1322 proteins in 8 plasma samples associated with low HER2/neu expression and in 12 associated with high HER2/neu expression revealed that the levels of 14 predicted HER2/neu transduction efficiency.  Conclusion: The manufacture of adHER2/neu DC using autologous plasma as a media supplement resulted in inconsistent HER2/neu expression. It is likely that variability in the levels of multiple proteins in autologous plasma contributed to low HER2/neu expression.

overall_design: The adHER2/neu DCs manufactured with healthy donor monocytes and patient #13 plasma, AB plasma or a mixture containing 50% AB plasma and 50% patient #13 plasma were also analyzed by global gene expression analysis, total 9 samples

first: Ping

last: Jin

first: Wenjing

last: Chen

first: Jiaqiang

last: Ren

first: Steven

first: Lauren

last: Wood

first: Yingdong

last: Zhao

first: Alan

last: Remaley

first: Chauha

last: Pham

first: Sheena

last: Lian

first: Shutong

last: Liu

first: Hui

last: Highfill

first: Jay

last: Berzofsky

first: David

last: Stroncek


title: Expression data from superficial zone cells of articular cartilage (SFZ) cells treated with retinoic acid

status: Public on Dec 17 2018

city: Suita

first: Yoshifumi

last: Takahata

state: Osaka

department: Dentistry

country: Japan

institute: Osaka University

summary: To identify downstream transcription factors induced by retinoic acid, we stimulated SFZ cells with 10 μM retinoic acid for 24 hours and performed microarray analysis.

overall_design: Superficial zone cells of articular cartilage (SFZ) were prepared from femur and tibial joint of postnatal 4days ICR mice. SFZ cells were cultured with or without 10 μM retinoic acid for 24 hours, and subsequent isolation of total RNA for Affymetrix Mouse Genome 430  2.0 array.


title: GATA-6 and NFkB Repress Caveolins Transcription in Bladder Smooth Muscle Hypertrophy

city: Philadelphia

first: Ettickan

last: Boopathi

state: Pennsylvania

address: 1020 Locust Street

department: Medicine

country: USA

institute: THOMAS Jefferson University

summary:
Microarray analysis of bladder RNA revealed down-regulation of CAV1, CAV2 and CAV3 gene transcription in both mice with obstruction-induced BSM hypertrophy, and in men with benign prostatic hyperplasia
Knockout of NF-κB subunits or shRNA-mediated knockdown of GATA-6 in BSM increased CAV1, CAV2 and CAV3 transcription and promoter activity.

overall_design: In this study, we performed a comprehensive analysis of genes regulation under conditions relevant to BSM hypertrophy and obstructive bladder disease.

first: Samuel

last: Chacko

first: Stephen

middle: A

last: Zderic

first: Chellappagounder

last: Thangavel

first: Sankar

last: Addya


title: Promoter or enhancer activation by CRISPRa rescues haploinsufficiency caused obesity

city: San Francisco

first: Walter

last: Eckalbar

state: CA

address: 513 Parnassus Ave MSB-813

institute: University of California, San Francisco

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Haploinsufficiency, having only one functional copy of a gene, leads to a wide-range of human diseases. Using obesity as a disease model, we tested whether haploinsufficiency can be rescued by CRISPR-mediated activation (CRISPRa) of the normal allele. Haploinsufficiency of either SIM1 or MC4R, results in severe obesity in humans and mice. In transgenic mice, CRISPRa targeting of the Sim1 promoter or its ~270kb distant hypothalamic enhancer, rescued the obesity phenotype in Sim1 heterozygous mice. Interestingly, despite using a ubiquitous promoter for CRISPRa, Sim1 was upregulated only in tissues where the promoter or enhancer are active, suggesting that cis-regulatory elements can determine CRISPRa tissue-specificity. To evaluate the potential therapeutic use of CRISPRa, we injected CRISPRa-rAAV into the hypothalamus, leading to reversal of the obesity phenotype in Sim1 and Mc4r heterozygous mice. Our results show that CRISPRa can be developed as a gene regulation therapy (GRT) to treat altered gene dosage diseases.

overall_design: RNA-seq and ChIP-seq experiments to confirm on-target CRISPRa binding and activation as well as to identify potential off-target sites.

first: Nadav

last: Ahituv


title: The transcriptome landscape of the carcinogenic treatment response in the blind mole rat: Insights into cancer resistance mechanisms [miRNA-seq]

status: Public on Dec 16 2018

city: Berlin

first: Robert

last: Altwasser

address: Robert-Rössle-Str. 10

department: AG Di Virgilio

country: Germany

institute: Max-Delbrück-centrum

type: Non-coding RNA profiling by high throughput sequencing

summary:
Background: Spalax, the blind mole rat, developed an extraordinary cancer resistance during 40 million years of evolution in a subterranean, hypoxic, thus DNA damaging, habitat. In 50 years of Spalax research, no spontaneous cancer development has been observed. The mechanisms underlying this resistance are still not clarified. We investigated the genetic difference between Spalax and mice that might enable the Spalax relative resistance to cancer development. We compared Spalax and mice responses to a treatment with the carcinogen 3-Methylcholantrene, as a model to assess Spalax’ cancer-resistance.
Results: We compared RNA-Seq data of untreated Spalax to Spalax with a tumor and identified a high number of differentially expressed genes. We filtered these genes by their expression in tolerant Spalax that resisted the 3MCA, and in mice, and found 25 genes with a consistent expression pattern in the samples susceptible to cancer among species.   Contrasting the expressed genes in Spalax with benign granulomas to those in Spalax with malignant fibrosarcomas elucidated significant differences in several pathways, mainly the extracellular matrix and the immune system. We found a central cluster of ECM genes that differ greatly between conditions.   Further analysis of these genes revealed potential drug targets and associated microRNAs.  We also show that in Spalax has higher levels of gene expression of some DNA repair pathways than other murines, like the majority of Fanconi Anemia pathway.
Conclusion: The comparison of the treated with the untreated tissue revealed a regulatory complex that might give an answer how Spalax is able to restrict the tumor growth. By strengthening the extracellular matrix, the possible growth is limited, and the proliferation of cancer cells was prevented. We hypothesize that this regulatory cluster plays a major role in the cancer resistance of Spalax.  Furthermore, we identified 25 additional candidate genes that show a distinct expression pattern in untreated or tolerant Spalax compared to animals that developed a growth, either benign or malignant. While further study is necessary, we believe that these genes may be used as markers in cancer detection.

sample_organism:
Mus musculus
Nannospalax ehrenbergi

platform_organism:
Mus musculus
Nannospalax ehrenbergi

overall_design: 12 Spalax and 6 mice were used. Animals were treated with a single injection of 3MCA as follows: 200 μg/200 μl for mice; 1 mg/500 μl for Spalax. Animals used in this experiment were: six approximately 2-year-old Spalax individuals; six 10-year old or older Spalax individuals; six 3- to 4- month-old mice. Animals were observed once a week until tumors could be palpated, and then two to three times a week.

first: Arnon

last: Paz

first: Abraham

last: Korol

first: Irena

last: Manov

first: Aaron

last: Avivi

first: Imad

last: Shams


title: The transcriptome landscape of the carcinogenic treatment response in the blind mole rat: Insights into cancer resistance mechanisms

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

overall_design: Refer to individual Series


title: The transcriptome landscape of the carcinogenic treatment response in the blind mole rat: Insights into cancer resistance mechanisms [RNA-seq]

summary:
Background: Spalax, the blind mole rat, developed an extraordinary cancer resistance during 40 million years of evolution in a subterranean, hypoxic, thus DNA damaging, habitat. In 50 years of Spalax research, no spontaneous cancer development has been observed. The mechanisms underlying this resistance are still not clarified. We investigated the genetic difference between Spalax and mice that might enable the Spalax relative resistance to cancer development. We compared Spalax and mice responses to a treatment with the carcinogen 3-Methylcholantrene, as a model to assess Spalax’ cancer-resistance.
Results: We compared RNA-Seq data of untreated Spalax to Spalax with a tumor and identified a high number of differentially expressed genes. We filtered these genes by their expression in tolerant Spalax that resisted the 3MCA, and in mice, and found 25 genes with a consistent expression pattern in the samples susceptible to cancer among species. Contrasting the expressed genes in Spalax with benign granulomas to those in Spalax with malignant fibrosarcomas elucidated significant differences in several pathways, mainly the extracellular matrix and the immune system. We found a central cluster of ECM genes that differ greatly between conditions. Further analysis of these genes revealed potential drug targets and associated microRNAs.We also show that in Spalax has higher levels of gene expression of some DNA repair pathways than other murines, like the majority of Fanconi Anemia pathway.
Conclusion: The comparison of the treated with the untreated tissue revealed a regulatory complex that might give an answer how Spalax is able to restrict the tumor growth. By strengthening the extracellular matrix, the possible growth is limited, and the proliferation of cancer cells was prevented. We hypothesize that this regulatory cluster plays a major role in the cancer resistance of Spalax.  Furthermore, we identified 25 additional candidate genes that show a distinct expression pattern in untreated or tolerant Spalax compared to animals that developed a growth, either benign or malignant. While further study is necessary, we believe that these genes may be used as markers in cancer detection.


title: ZBTB10 binds the telomeric variant repeat TTGGGG and interacts with TRF2

city: Mainz

first: Falk

last: Butter

state: Germany

address: Ackermannweg 4

department: Quantitative Proteomics

institute: Institute of Molecular Biology gGmbH


title: ZBTB10 binds the telomeric variant repeat TTGGGG and interacts with TRF2 [DNA-Seq validation of KO]

summary: In order to investigate changes upon ZBTB10 depletion, we used CRISPR/Cas9 to induce a ZBTB10 knockout in HEK293 and U2OS cells.

overall_design: ZBTB10 knockouts were generated using three different guide RNAs targeting the second exon of the ZBTB10 gene. HEK293 and U2OS cells were selected in 750 ng/mL puromycin after transfection and gDNA was extracted. A circa 1100 bp long target sequence around the cut locus was amplified by PCR and Cas9 activity was tested in a T7 endonuclease assay. After confirming Cas9 activity, single cell sorting was performed and cells were expanded to screen for ZBTB10 knockout clones by Western blot using an anti-ZBTB10 antibody (Supplementary Table 1).

first: Alina

last: Bluhm

first: Michal

last: Levin


title: FoxA1 and FoxA2 are required for gastric differentiation in NKX2-1-negative lung adenocarcinoma [single cell analysis]

city: Salt Lake City

first: Eric

last: Snyder

state: UT

address: 2000 Circle of Hope Drive

department: Pathology

institute: University of Utah, Huntsman Cancer Institute

summary: Profound changes in cancer cell identity can alter malignant potential and therapeutic response.  Loss of the pulmonary lineage specifier NKX2-1 augments the growth of KRAS-driven lung adenocarcinoma and causes pulmonary to gastric transdifferentiation. Here we show that the transcription factors FoxA1 and FoxA2 are required for initiation of mucinous NKX2-1-negative lung adenocarcinomas in the mouse and for activation of their gastric differentiation program.  Foxa1/2 deletion severely impairs tumor initiation and causes a proximal shift in cellular identity, yielding tumors expressing markers of the squamocolumnar junction of the gastrointestinal tract. In contrast, stochastic loss of FoxA1/2 expression in NKX2-1-negative tumors is associated with keratinizing squamous differentiation.  Using sequential in vivo recombination, we find that FoxA1/2 loss in established KRAS-driven neoplasia is sufficient for direct induction of keratinizing squamous cell carcinomas in the lung. Thus, NKX2-1, FoxA1 and FoxA2 coordinately regulate the growth and identity of lung adenocarcinoma in a context-specific manner.

overall_design: Murine lung tumor cells of differing genotypes were isolated by FACS and subjected to single cell analysis using the Fluidigm C1 platform.

middle: L


title: FoxA1 and FoxA2 are required for gastric differentiation in NKX2-1-negative lung adenocarcinoma


title: Lysosomal signaling licenses embryonic stem cell differentiation via inactivation of Tfe3

status: Public on Dec 18 2018

city: Basel

first: Joerg

last: Betschinger

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute

summary: Self-renewal and differentiation of pluripotent murine embryonic stem cells (ESCs) is regulated by extrinsic signaling pathways. It is less clear whether cellular metabolism instructs developmental progression. In an unbiased genome-wide CRISPR/Cas9 screen, we identified components of a conserved amino acid-sensing pathway as critical drivers of ESC differentiation. Functional analysis revealed that lysosome activity, the Ragulator protein complex, and the tumor-suppressor protein Folliculin enable the Rag GTPases C and D to bind and seclude the bHLH transcription factor Tfe3 in the cytoplasm. In contrast, ectopic nuclear Tfe3 represses specific developmental and metabolic transcriptional pro- grams that are associated with peri-implantation development. We show differentiation-specific and non-canonical regulation of Rag GTPase in ESCs and, importantly, identify point mutations in a Tfe3 domain required for cytoplasmic inactivation as potentially causal for a human developmental disorder. Our work reveals an instructive and biomedically relevant role of metabolic signaling in licensing embryonic cell fate transitions.

overall_design: Mouse embryonic stem and differentiated cell mRNA profiles of  wild type, Flcn KO, LT1 KO and ectopic nuclear Tfe3 cell lines were generated by deep sequencing, in duplicates, using Illumina HiSeq2500.

first: Daniela

last: Mayer

first: Melanie

last: Rittirsch

first: Michael

middle: B

last: Stadler

first: Sebastien

last: Smallwood

first: Sophie

last: Dessus-Babus

first: Kirsten

last: Jacobeit

first: Tim

last: Roloff


title: Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells [ATAC-seq]

city: Cincinnati

first: Emily

middle: R

last: Miraldi

state: Ohio

address: 3333 Burnet Avenue, MLC 7038

department: Immunobiology and Biomedical Informatics

institute: Cincinnati Children's Hospital Medical Center

summary: Transcriptional regulatory networks (TRNs) provide insight into cellular behavior by describing interactions between transcription factors (TFs) and their gene targets. The Assay for Transposase Accessible Chromatin (ATAC)-seq, coupled with transcription-factor motif analysis, provides indirect evidence of chromatin binding for hundreds of TFs genome-wide. Here, we propose methods for TRN inference in a mammalian setting, using ATAC-seq data to influence gene expression modeling.   We rigorously test our methods in the context of T Helper Cell Type  17 (Th17) differentiation, generating new ATAC-seq data to complement existing Th17 genomic resources (plentiful gene expression data, TF knock-outs and ChIP-seq experiments).  In this resource-rich mammalian setting our extensive benchmarking provides quantitative, genome-scale evaluation of TRN inference combining ATAC-seq and RNA-seq data. We refine and extend our previous Th17 TRN, using our new TRN inference methods to integrate all Th17 data (gene expression, ATAC-seq, TF KO, ChIP-seq). We highlight new roles for individual TFs and groups of TFs (“TF-TF modules”) in Th17 gene regulation.  Given the popularity of ATAC-seq (a widely adapted protocol with high resolution and low sample input requirements),  we anticipate that application of our methods will improve TRN inference in new mammalian systems and be of particular use for rare, uncharacterized cell types.

overall_design: Chromatin accessibility (ATAC-seq) of Th17-, Treg-, Th2-, Th0-polarized CD4 T Cells (from 2-48hrs, including MAF and STAT3 KO)

first: Maria

last: Pokrovskii

first: Richard

last: Bonneau

first: Dan

last: Littman


title: Agilent 8x60K Custom Exon array of human temporal cortical tissue samples with varying degree of Alzheimer's Disease (AD)-related neurofibrillary pathology

city: Kuopio

first: Mikael

last: Marttinen

address: Yliopistonranta 1E

department: Biomedicine

country: Finland

institute: University of Eastern Finland

summary: In this study, we coupled microarray-based transcriptomics and MS-based phosphoproteomics assay to determine mRNA, protein, and phosphopeptide expression levels from 71 autopsied temporal cortical samples, with varying degree of Alzheimer's Disease (AD)-related neurofibrillary pathology. With computational analysis, we identified disease-related transcript, protein and phosphopeptide expression patterns, associated with distinct biological processes and cell types.

overall_design: 71 human temporal cortical tissue samples were divided into 7 groups based on Braak staging (degree of AD-related neurofibrillary pathology) indicating the degree of disease severity. From 60 of these samples, transcripts were identified by microarray analysis. Additionally, utilizing liquid chromatography tandem mass spectrometry (LC-MS/MS) phospho-proteomics, proteins and phosphopeptides were identified from 36 samples (Data found in PRIDE). Furthermore, APOE genotype, Alpha-, beta-, and gamma-secretase activity, and amyloid-beta 42 levels were determined from the tissue samples.

first: Jussi

last: Paananen


title: Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells


title: Lsd1 as a therapeutic target in Gfi1-activated medulloblastoma [ChIP-seq]

status: Public on Dec 15 2018

city: HEIDELBERG

first: Paul

middle: A.

last: Northcott

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

summary:
Drugs that modify the epigenome are powerful tools for treating cancer, but these drugs often have pleiotropic effects, and identifying patients who will benefit from them remains a major clinical challenge. Here we show that medulloblastomas driven by the transcription factor Gfi1 are exquisitely dependent on the enzyme lysine demethylase 1 (Kdm1a/Lsd1). We demonstrate that Lsd1 physically associates with Gfi1, and that these proteins cooperate to inhibit genes involved in neuronal commitment and differentiation. We also show that Lsd1 is essential for Gfi1-mediated transformation: Gfi1 proteins that cannot recruit Lsd1 are unable to drive tumorigenesis and genetic ablation of Lsd1 markedly impairs tumor growth in vivo. Finally, pharmacological inhibitors of Lsd1 potently inhibit growth of Gfi1-driven tumors. These studies provide important insight into the mechanisms by which Gfi1 contributes to tumorigenesis, and identify Lsd1 inhibitors as promising therapeutic agents for Gfi1-driven medulloblastoma.
ChIP-seq data generated for n=2 MG (Myc/Gfi1) murine medulloblastomas. ChIP was independently performed for Gfi1 and Lsd1 on the same chromatin extracts.

overall_design: MG medulloblastoma tumors were surgically resected, frozen, and subsequently subjected to fixation, chromatin extraction, and ChIP using antibodies for Gfi1 and Lsd1.

first: Robert

middle: J

last: Wechsler-Reya


title: Lsd1 as a therapeutic target in Gfi1-activated medulloblastoma


title: Leveraging chromatin accessibility for transcriptional regulatory network inference in T Helper 17 Cells [RNA-seq]

overall_design: Gene expression (RNA-seq) of naive and Th17- and Th0-polarized CD4 T Cells

last: Ciofani

first: Jason

last: Hall

first: June-Yong

last: Lee


title: Loss of miR-83 extends lifespan and affects target gene expression in an age-dependent manner in Caenorhabditis elegans

city: Hefei

first: Ge

last: Shan

state: Anhui

address: 443 Huangshan Road

department: School of Life Sciences

country: China

institute: University of Science and Technology of China

summary: We have identified a role of the C. elegans miR-83 in regulating lifespan. mir-83 mutants exhibit an extended lifespan, and its overexpression is sufficient to decrease the prolonged lifespan of the mutants. We observed an upregulation in the expression of sets of miR-83 targets in young mir-83 mutant adults.  However, in older mir-83 mutant adults, a different set of genes are upregulated. In vivo assays show that miR-83 regulates expression of a number of targets, including din-1, spp-9 and col-178. We show that daf-16 and din-1 are required for the lifespan extension of mir-83 mutants. The regulation of din-1 by miR-83 during aging results in the differential expression of din-1 targets, such as gst-4 and gst-10. In daf-2 mutants, the expression levels of miR-83 are significantly reduced, as compared to wildtype animals. Our results identify a role of miR-83 in modulating lifespan in C. elegans, and provide molecular insights into its functional mechanism.

overall_design: Worms were cultured on FuDR-containing NGM plates until adult day 4 and day 12. Total RNA was extracted and then sequenced.

first: Emmanuel

middle: E

last: Dzakah

first: Shuai

last: Wei


title: RNA sequencing after forced turnover of adult and aged microglia

city: Columbus

first: Kristina

middle: Grace

last: Witcher

state: OH

address: 460 Medical Center Dr

department: Neuroscience

institute: Ohio State University

summary: The goal of this study was to determine whether depletion and repopulation of microglia in adult and aged mice reversed age-related immune priming.

overall_design: Adult (2mo) and Aged (22mo) BALB/c mice were administered control diet or chow containing PLX5562, a colony-stimulating factor 1 receptor antagonist, for 3 weeks to eliminate microglia. Mice were then fed control diet for 3 weeks to allow for microglial repopulation. RNA was extracted from either FAC-sorted microglia (CD11b+/CD45int) or a 1mm coronal brain section. RNA sequencing was performed and sequences were aligned with STAR and normalized counts and differential gene expression were determined using DESeq2 in R.

first: Jonathan

middle: P

last: Godbout


title: Transcriptomes of CD31+CD34+HEPs with different expression of CD105 derived from human early hematopoietic differentiation by RNA Sequencing

city: Tianjin

first: Jiaxi

last: Zhou

state: Tianjin

address: 288# Nanjing Road, He ping district

institute: PUMC

summary:
Purpose: The goals of this study are to dessect the molecular signature of CD31+CD34+HEPs with different expression of CD105 ,and to explore the regulators such as signaling and transcription factors of CD105+ cells' generation.
Methods: mRNA profiles of HEPs samples collected at day4 of  hematopoietic differentiation were generated by deep sequencing using Illumina HiSeq 2000. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays
Conclusions: The CD31+CD34+CD105-HEPs possess hematopoietic potential whereas the CD31+CD34+CD105+HEPs possess endothelial potential. In addition, the generation of CD105+cells were regulated by TGFbeta signaling and ETS1.

first: Hongtao

last: Wang


title: Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis

city: Chicago

first: Alexander

middle: V

last: Misharin

state: IL

address: 240 E Huron

department: Pulmonary and Critical Care

institute: Northwestern University

summary: Pulmonary fibrosis is a heterogeneous syndrome in which fibrotic scar replaces normal lung tissue. We performed massively parallel single-cell RNA-Seq on lung tissue from eight lung transplant donors and eight patients with pulmonary fibrosis. Combined with in situ RNA hybridization, with amplification, these data provide a molecular atlas of disease pathobiology. We identified a distinct, novel population of profibrotic alveolar macrophages exclusively in patients with fibrosis. Within epithelial cells, the expression of genes involved in Wnt secretion and response was restricted to non-overlapping cells. We identified rare cell populations including airway stem cells and senescent cells emerging during pulmonary fibrosis. Analysis of a cryobiopsy specimen from a patient with early disease supports the clinical application of single-cell RNA-Seq to develop personalized approaches to therapy. This dataset contains single-cell RNA-seq data generated from the lungs of the two naive mice, human data for this study has been submitted to dbGap/SRA.

overall_design: Single-cell suspension from two 4 mo old C57Bl/6 male mice was prepared and single cell RNA-seq libraries were generated using 3' V2 chemistry kit on Chromium Single cell controller (10x Genomics).

last: Reyfman

first: James

middle: M

last: Walter

first: Nikita

last: Joshi

first: Alexandra

middle: C

last: McQuattie

first: Kishore

last: Anekalla

first: GR

middle: S

last: Budinger


title: Diabetes Remission Using Glucose-Responsive Insulin-Producing Human alpha-Cells

city: Kyoto

first: Kenichiro

last: Furuyama

state: Kyoto

address: 53 Shogoinkawahara-cho, Sakyo-ku

department: Life Science Frontiers

institute: CiRA, Kyoto University

summary: Natural and stable cell identity switches, where terminally-differentiated cells convert into different cell-types when stressed, represent a widespread regenerative strategy in animals, yet they are poorly documented in mammals. In mice, some glucagon-producing pancreatic α-cells become insulin expressers upon ablation of insulin-secreting β-cells, promoting diabetes recovery. Whether human islets also display this plasticity for reconstituting β-like cells, especially in diabetic conditions, remains unknown. Here we show that two different islet non-β-cell types, α- and γ–cells, obtained from deceased non-diabetic or diabetic human donors can be lineage-traced and induced to produce insulin and secrete it in response to glucose. When transplanted into diabetic mice, converted human α-cells reverse diabetes and remain producing insulin even after 6 months. Insulin-producing α-cells maintain α-cell markers, as seen by deep transcriptomic and proteomic characterization, and display hypo-immunogenic features when exposed to T-cells derived from diabetic patients. These observations provide conceptual evidence and a molecular framework for a mechanistic understanding of in situ cell plasticity in islet cells, as well as in other organs, as a therapy for degenerative diseases by fostering the highly-regulated intrinsic cell regeneration.

overall_design: Single-cell transcriptomic profiles of human pancreatic ?-cells that convert  into insulin-producing cells were generated by deep sequencing using Illumina Hi-seq 4000.

first: Pedro

last: Herrera


title: Generation and characterization of phosphosite mutants in S. cerevisiae

city: Cambridge

last: Beltrao

address: Wellcome Genome Campus

country: United Kingdom

institute: EMBL-EBI

summary: The functional relevance of phosphosites currently lacks a systematic assessment. Here a large number of S. cerevisiae phosphosites are mutated to alanine and its impact on cellular fitness is measured. Gene expression changes between strains harbouring the mutated phosphosites is compared against the wild type and the corresponding gene deletion.

overall_design: Each sample has been analyzed in triplicate. All samples were harvested when cultures reached O.D. of 0.4 (at 600 nanometers).

first: Cristina

last: Vieitez

first: Bede

last: Busby

first: David

last: Ochoa

first: Marco

last: Galardini

first: Ferris

last: Jung

first: Nayara

middle: T

last: Doimo de Azevedo

first: Athanasios

last: Typas


title: Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis II

last: Misharin

summary: Pulmonary fibrosis is a heterogeneous syndrome in which fibrotic scar replaces normal lung tissue. We performed massively parallel single-cell RNA-Seq on lung tissue from eight lung transplant donors and eight patients with pulmonary fibrosis. Combined with in situ RNA hybridization, with amplification, these data provide a molecular atlas of disease pathobiology. We identified a distinct, novel population of profibrotic alveolar macrophages exclusively in patients with fibrosis. Within epithelial cells, the expression of genes involved in Wnt secretion and response was restricted to non-overlapping cells. We identified rare cell populations including airway stem cells and senescent cells emerging during pulmonary fibrosis. Analysis of a cryobiopsy specimen from a patient with early disease supports the clinical application of single-cell RNA-Seq to develop personalized approaches to therapy.

overall_design: Single-cell suspensions from eight donor lungs and nine lungs from patients with various forms of pulmonary fibrosis were prepared and single cell RNA-seq libraries were generated using 3' V2 chemistry kit on Chromium Single cell controller (10x Genomics). This GEO submission contains only processed data (raw counts tables in HDF5 format), raw data (FASTQ files) available from dbGaP/SRA (phs001750.v1.p1).

first: Paul


title: RNA-seq analysis for resistance to PI3K inhibition in Glioblastoma (GBM)

status: Public on Dec 14 2018

city: Houston

first: Dimpy

last: Koul

state: TX

address: 6767 Bertner Ave

institute: MD Anderson Cancer Center

summary: The goal of this study is to identify the pathway alterations driving the adaptive resistance to PI3K inhibition in GBM. We generated the resistant cell lines through a patient-derived in vivo glioma sphere-forming cell (GSC) model.  We performed RNA-seq on the paired GSC samples including the parental and resistant groups. Libraries were sequenced with an average coverage for each tumor of 50x on the Hiseq4000 platform from Illumina, using 76 nt pair-ended reads. RNA-seq raw data were pre-processed using PRADA. PRADA aligned RNA-seq reads to a composite reference database composed of whole genome and transcriptome sequences; we used the hg19 human genome assembly, together with the Ensembl64 transcriptome version. Transcripts were filtered for size and protein-coding genes. Expression data were normalized to reads per kilobase per million reads, and these values were log2-transformed for further analyses.

overall_design: Examination of gene expression profile in the parental and resistant GSCs.

first: Emmanuel

last: Martinez-Ledesma


title: Shoot transcriptomic response is more sensitive to a 14 day water deficit than root transcriptomic response in Vitis riparia

city: Brookings

first: Anne

last: Fennell

state: SD

address: 1390 College Ave

department: Plant Science

institute: South Dakota State University

summary: Drought has become an increasingly important constraint on grapevine sustainability due to global climate change. Vitis riparia, the only grapevine native to the upper Midwest region of the United States, is widely used in scion and rootstock breeding; however, it is not considered drought tolerant. In this study, RNA-Seq data were generated from grapevine root/shoot under WD and well-watered (control (C)) conditions to compare root signaling and shoot responses to water deficit.

overall_design: 36 grapevines were randomized into two groups:  water deficit (WD) and well-watered control (C).  Five days after randomization, differential water treatments began in replicates (3 vines/ replicate) of each treatment:  WD received no water and C received 2 L of tap water each day.  Root and shoot samples from the 14 d C and WD treatments were used for transcriptomic analysis, as this time point showed distinct physiological differences between treatments.

first: Vedbar

last: Khadka

first: Padmapriya

last: Swaminathan


title: Transcriptomic Alterations in Lung Adenocarcinoma Unveil New Mechanisms Targeted by the TBX2 Subfamily of Tumor Suppressor Genes

city: Beirut

first: Athar

last: Khalil

address: Bliss

department: Biochemistry and Molecular Genetics

country: Lebanon

institute: American University of Beirut

summary: T-box (TBX) transcription factors are evolutionary conserved genes and master transcriptional regulators. In mammals, TBX2 subfamily (TBX2, TBX3, TBX4, and TBX5) genes are expressed in the developing lung bud and tracheae. Our group previously showed that the expression of TBX2 subfamily was significantly high in human normal lungs, but markedly suppressed in lung adenocarcinoma (LUAD). To further elucidate their role in LUAD pathogenesis, we first confirmed abundant expression of protein products of the four members by immunostaining in adult human normal lung tissues. We also found overall suppressed expression of these genes and their corresponding proteins in a panel of human LUAD cell lines. Transient over-expression of each of the genes in human (NCI-H1299), and mouse (MDA-F471) derived lung cancer cells was found to significantly inhibit growth and proliferation as well as induce apoptosis. Genome-wide transcriptomic analyses on NCI-H1299 cells, overexpressing TBX2 gene subfamily, unraveled novel regulatory pathways. These included, among others, inhibition of cell cycle progression but more importantly activation of the histone demethylase pathway. When using a pattern-matching algorithm, we showed that TBX's overexpression mimic molecular signatures from azacitidine treated NCI-H1299 cells which in turn are inversely correlated to expression profiles of both human and murine lung tumors relative to matched normal lung. In conclusion, we showed that the TBX2 subfamily genes play a critical tumor suppressor role in lung cancer pathogenesis through regulating its methylating pattern, making them putative candidates for epigenetic therapy in LUAD.

overall_design: Genetic profiling of the transient overexpression of TBX2-5 in NCI-H1299 cells

first: Nehme

last: El-Hachem

first: Georges

last: Nemer


title: RNA-seq data for non-targeting siRNA and lncRNA LOL siRNA transfection in MCF-7 cells

city: Shanghai

first: Wei

last: Sun

address: Dongan Road 270

department: Department of Musculoskeletal Surgery

institute: Fudan University Shanghai Cancer Center

summary: To  elucidate which portions of signaling pathways LOL influences in luminal breast cancer, RNA-seq analysis was performed in siLOL MCF-7 cell lines. Eight hundred eighty-three downregulated genes and 1182 upregulated genes (fold change ≥1.5) were detected after LOL knockdown. Gene set enrichment analysis (GSEA) of hallmarks indicated that the gene sets related to DNA_Repair, G2M_Checkpoint, E2F_Targets and MYC_Targets were positively correlated with LOL downregulation.

overall_design: Examine the gene expression pattern in NC and LOL KD MCF-7 cells, and compare the gene expression to find out the differentially expressed genes.

first: Zhiming

last: Shao


title: ZBTB10 binds the telomeric variant repeat TTGGGG and interacts with TRF2 [RNA-Seq]

first: Falk

last: Butter

summary: To study if ZBTB10 influences gene expression, we used CRISPR/Cas9 knockout HEK293 and U2OS cells to compare transcript levels between WT and KO.

overall_design: After validation of ZBTB10 knockout clones by DNA-Seq and by Western blot, we extracted total mRNA from WT and KO clones of HEK293 and U2OS cells for RNA sequencing and characterized transcriptomic changes between WT and KO phenotypes.

first: Alina

last: Bluhm

first: Michal

last: Levin


title: Transcriptome sequencing elucidates gene modules in microglia

city: Carlsbad

first: Christine

last: Cho

state: California

address: 2855 Gazelle Ct

institute: Ionis Pharmaceuticals

summary: Microglia are multifunctional cells that are important for brain development and homeostasis. Despite the growing evidence of their complexity, the field lacks a unified system for categorizing the many microglial states. In an effort to develop a comprehensive classification system, we profiled transcriptomes of mouse microglia in 96 different stimulus conditions. We generated fine-resolution gene modules that are robustly preserved across datasets by employing a two-step clustering approach. These modules served as the basis for a combinatorial code that we then used to characterize microglial activation under inflammatory stimulus conditions in vitro. Many of the modules were preserved in vivo, and were differentially regulated during acute inflammation and in aging. In summary, the microglial gene modules presented here are a novel resource for classifying and characterizing microglial states in health and disease.

overall_design: Transcriptome profiles from microglia activated in 96 different stimulus conditions in vitro and 2 conditions in vivo. Each condition had a minimum of 3 replicates, for a total of 922 samples.


title: Knockdown of heterochromatin protein 1 binding protein 3 recapitulates phenotypic, cellular, and molecular features of aging

city: Bar Harbor

first: Catherine

last: Kaczorowski

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

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

overall_design: Refer to individual Series


title: Knockdown of heterochromatin protein 1 binding protein 3 recapitulates phenotypic, cellular, and molecular features of aging [miRNA-Seq]

summary: Identifying genetic factors that modify an individual’s susceptibility to cognitive decline in aging is critical to understanding biological processes involved and mitigating risk associated with a number of age-related disorders. Recently, heterochromatin protein 1 binding protein 3 (Hp1bp3) was identified as a mediator of cognitive aging. Here we provide a mechanistic explanation for these findings and show that targeted knockdown of Hp1bp3 in the hippocampus by 50-75% is sufficient to induce cognitive deficits and transcriptional changes reminiscent of those observed in aging and Alzheimer’s disease brains. Specifically, neuroinflammatory-related pathways become activated following Hp1bp3 KD in combination with a robust decrease in genes involved in synaptic activity and neuronal function. To test the hypothesis that Hp1bp3 mediates susceptibility to cognitive deficits via a role in neuronal excitability, we performed slice electrophysiology demonstrate transcriptional changes after Hp1bp3 KD manifest functionally as a reduction in hippocampal neuronal intrinsic excitability and synaptic plasticity. In addition, as Hp1bp3 is a known mediator of miRNA biogenesis, here we profile the miRNA transcriptome and identify mir-223 as a putative regulator of a portion of observed mRNA changes, particularly those that are inflammatory-related. In summary, work here identifies Hp1bp3 as a critical mediator of aging-related changes at the phenotypic, cellular, and molecular level and will help inform the development of therapeutics designed to target either Hp1bp3 or its downstream effectors in order to promote cognitive longevity.

overall_design: Viral vectors encoding either shRNA for Hp1bp3 (AAV9-shRNA-Hp1bp3) or a scrambled control (AAV-scrmb-shRNA) were delivered bilaterally into the hippocampus of adult (3-5 month old) C57BL/6J and DBA/2J mice. Three male mice from each group were used for sequencing. Briefly, each mouse was anesthetized using isoflurane, brains were quickly removed, and the hippocampus immediately dissected and snap-frozen in liquid nitrogen. Samples were kept at -80 until further use. RNA quality was evaluated using a BioAnalyzer, libraries prepared, and sequenced on a Illumina HiSeq 2500. A pairs of miRNA samples given identical barcodes during the initial sequencing. All samples were re-sequenced and where available, fastq files from both runs were concatenated, providing expanded sequencing depth for 10/12 samples.

first: Sarah

last: Neuner

first: Shengyuan

last: Ding


title: FoxA1 and FoxA2 are required for gastric differentiation in NKX2-1-negative lung adenocarcinoma [total RNA-seq analysis]

city: Salt Lake City

first: Eric

last: Snyder

address: 2000 Circle of Hope Drive

institute: University of Utah, Huntsman Cancer Institute

summary: Profound changes in cancer cell identity can alter malignant potential and therapeutic response.  Loss of the pulmonary lineage specifier NKX2-1 augments the growth of KRAS-driven lung adenocarcinoma and causes pulmonary to gastric transdifferentiation. Here we show that the transcription factors FoxA1 and FoxA2 are required for initiation of mucinous NKX2-1-negative lung adenocarcinomas in the mouse and for activation of their gastric differentiation program.  Foxa1/2 deletion severely impairs tumor initiation and causes a proximal shift in cellular identity, yielding tumors expressing markers of the squamocolumnar junction of the gastrointestinal tract. In contrast, stochastic loss of FoxA1/2 expression in NKX2-1-negative tumors is associated with keratinizing squamous differentiation.  Using sequential in vivo recombination, we find that FoxA1/2 loss in established KRAS-driven neoplasia is sufficient for direct induction of keratinizing squamous cell carcinomas in the lung. Thus, NKX2-1, FoxA1 and FoxA2 coordinately regulate the growth and identity of lung adenocarcinoma in a context-specific manner.

overall_design: Murine lung tumor cells of differing genotypes were isolated by FACS and subjected to total RNA-Seq.


title: The Translation of Non-Canonical Open Reading Frames Controls Mucosal Immunity

city: Boston

first: Lina

last: Kroehling

state: MA

address: 91 E Concord St

institute: Boston Unviersity

summary: We describe the identification of novel non-canonical ORFs in murine macrophages

overall_design: Using RNAseq, RiboTag RNA seq and Ribosome Profiling in Murine macrophages untreated and stimulated with LPS

first: Ruaidhri

last: Jackson


title: Liver transcriptomic and proteomic profiles of preweaning lambs are modified by milk replacer restriction

city: León

first: Alba

middle: Santos

last: Baza

state: León

address: Finca Marzanas, Grulleros

department: Nutrición y Producción de Herbívoros

country: Spain

institute: Instituto de Ganadería de Montaña (CSIC)

summary:
Purpose: The present study was designed to identify both differentially expressed (DE) genes  and differences in proteins accumulated in the liver tissues of suckling female lambs, thus trying to identify modified metabolic pathways as a consequence of milk restriction during the suckling period.
Methods: Forty Assaf lambs (average BW 4.7 kg) were penned individually, twenty of them were fed milk replacer (200 g dry matter/L) ad libitum (ADL; 192 mL/kg LBW) whereas the other group (restricted, RES) only received 120 mL/kg LBW. When they were 35 days old, four animals per group were slaughtered (8 lambs in total) and a piece of liver was excised for transcriptomic analysis. The liver transcriptome analysis was carried out using RNA sequencing methodology (RNA-seq).
Results: 386 DE genes were identified by RNA-seq, 198 of them being annotated genes in the KEGG pathway. Positive values of log2-fold change (log2FC) indicated that 210 genes were up-regulated in the liver of RES relative to the ADL group, whereas negative log2FC values denoted the down-regulation of 176 genes (P < 0.05).
Conclusions: According to the data obtained, a restricted milk intake during the suckling period of replacement lambs affects hepatic transcriptome and proteome associated with an altered metabolism of lipids and proteins, thus reducing feed efficiency of replacement period.

overall_design: A transcriptomic analysis was carried out using next-generation sequencing (RNA-seq) from liver samples: 4 animals from ADL group and 4 animals from RES group, 8 samples in total.

last: Santos

first: Francisco

last: Giráldez

first: Javier

last: Frutos

first: Sonia

last: Andrés


title: Different roles of E proteins in t(8;21) leukemia: E2-2 compromises the function of AETFC and negatively regulates leukemogenesis

first: Chun-hui

last: Xu

state: Shanghai

address: 197 Ruijin Road II

department: State Key Laboratory of Medical Genomics

institute: Shanghai Institute of Hematology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine

summary: The AML1-ETO fusion protein, generated by the t(8;21) chromosomal translocation, is causally involved in nearly 20% of acute myeloid leukemia (AML) cases. In leukemic cells, AML1-ETO resides in and functions through a stable protein complex, AETFC, that contains multiple transcription (co)factors. Among these AETFC components, HEB and E2A, two members of the ubiquitously expressed E proteins, directly interact with AML1-ETO, confer new DNA-binding capacity to AETFC, and are essential for leukemogenesis. However, the third E protein, E2-2, is specifically silenced in AML1-ETO–expressing leukemic cells, suggesting E2-2 as a negative factor of leukemogenesis. Indeed, ectopic expression of E2-2 selectively inhibits the growth of AML1-ETO–expressing leukemic cells, and this inhibition requires the bHLH DNA-binding domain. RNA-seq and ChIP-seq analyses reveal that, despite overlapping to some extent, the three E proteins differentially regulate many target genes, and, in particular, that E2-2 both redistributes AETFC to, and activates, some genes associated with dendritic cell differentiation. In AML patients, the expression of E2-2 is relatively lower in the t(8;21) subtype, and an E2-2 target gene, THPO, is identified as a potential predictor of relapse. In a mouse model of human t(8;21) leukemia, E2-2 suppression accelerates leukemogenesis. Taken together, these results reveal that, in contrast to HEB and E2A, which facilitate AML1-ETO–mediated leukemogenesis, E2-2 compromises the function of AETFC and acts as a negative regulator of leukemogenesis. The three E proteins thus define a heterogeneity of AETFC, which improves our understanding of the precise mechanism of leukemogenesis and assists development of diagnostic/therapeutic strategies.

overall_design: The three E proteins (E2-2, E2A and HEB) were tagged with HA and transduced into Kasumi-1 cells and the ChIP-seq was performed with an anti-HA antibody. These cells, as well as the control cells transduced with the MIGR1 vector, were also subjected to RNA-seq analysis.

last: Liu

first: Bowen

last: Rong

first: Chun-Hui

first: Fei

last: Lan

first: Lan

last: Wang

first: Xiao-Jian

last: Sun


title: Knockdown of heterochromatin protein 1 binding protein 3 recapitulates phenotypic, cellular, and molecular features of aging [RNA-Seq]

last: Kaczorowski

overall_design: Viral vectors encoding either shRNA for Hp1bp3 (AAV9-shRNA-Hp1bp3) or a scrambled control (AAV-scrmb-shRNA) were delivered bilaterally into the hippocampus of adult (3-5 month old) C57BL/6J and DBA/2J mice. Three male mice from each group were used for sequencing. Briefly, each mouse was anesthetized using isoflurane, brains were quickly removed, and the hippocampus immediately dissected and snap-frozen in liquid nitrogen. Samples were kept at -80 until further use. RNA quality was evaluated using a BioAnalyzer, libraries prepared, and sequenced on a Illumina HiSeq 2500. A pairs of mRNA samples given identical barcodes during the initial sequencing. All samples were re-sequenced and where available, fastq files from both runs were concatenated, providing expanded sequencing depth for 10/12 samples.


title: Widespread RNA editing dysregulation in Autism Spectrum Disorders II

city: Los Angeles

first: Grace

last: Xiao

address: 610 Charles E. Young Drive S

department: UCLA Department of Integrative Biology and Physiology

institute: UCLA

summary: Autism spectrum disorder (ASD) is a neurodevelopmental disease with complex heterogeneity and aberrations in multiple levels of neurobiology. Recently, our understanding of the molecular abnormalities in ASD has been greatly expanded through transcriptomic analyses of postmortem brains. However, a crucial molecular pathway involved in synaptic development, RNA editing, has not yet been studied on a genome-wide scale. Here we profiled the global patterns of adenosine-to-inosine (A-to-I) editing in a large cohort of ASD cortices and cerebella. Strikingly, we observed a global bias of hypoediting in ASD brains, common to different brain regions and involving many genes with critical neurological function. The large-scale RNA editing changes allowed us to reveal novel insights of RNA editing regulation. Through genome-wide protein-RNA binding analyses and detailed molecular assays, we show that the Fragile X proteins, FMRP and FXR1P, interact with ADAR protens and modulate A-to-I editing. Furthermore, we observed convergent patterns of RNA editing alterations between ASD and Fragile X syndrome, thus establishing RNA editing as a novel molecular link underlying these two highly related diseases. Our findings support a role for RNA editing dysregulation in ASD pathophysiology and highlight novel mechanisms for RNA editing regulation.

overall_design: RNA-seq to examine RNA editing in Fragile X patients

first: Stephen

last: Tran

first: Hyun-Ik

last: Jun

first: Jae

middle: H

last: Bahn

first: Adel

last: Azghadi

first: Gokul

last: Ramaswami

last: Van Nostrand

first: Thai

last: Nguyen

first: Yun-Hua

last: Hsiao

first: Chang

last: Lee

first: Gabriel

last: Pratt

first: Gene

middle: W

last: Yeo

first: Daniel

last: Geschwind

first: Xinshu


title: Local Genomic Features Predict the Distinct and Overlapping Binding Patterns of the bHLH‐Zip Family Oncoproteins MITF and MYC‐MAX

city: Urbana

first: Miroslav

last: Hejna

state: Illinois

address: 1110 West Green Street

department: Department of Physics

institute: University of Illinois

summary: MITF and MYC are well‐known oncoproteins and members of the basic helix‐loop‐helix leucine zipper (bHLH‐Zip) family of transcription factors (TFs) recognizing hexamer E‐box motifs. MITF and MYC not only share the core binding motif, but are also the two most highly expressed bHLH‐Zip transcription factors in melanocytes, raising the possibility that they may compete for the same binding sites in select oncogenic targets. Mechanisms determining the distinct and potentially overlapping binding modes of these critical oncoproteins remain uncharacterized. We introduce computational predictive models using local sequence features, including a boosted convolutional decision tree framework, to distinguish MITF vs. MYC‐MAX binding sites with up to 80% accuracy genome wide. Select E‐box locations that can be bound by both MITF and MYC‐MAX form a separate class of MITF binding sites characterized by differential sequence content in the flanking region, diminished interaction with SOX10, higher evolutionary conservation, and less tissue‐specific chromatin organization.

overall_design: Investigation of MITF vs MYC-MAX binding in melanoma using ChIP-seq data.

first: Wooyoung

last: Moon

first: Jeffrey

last: Cheng

first: Akinori

last: Kawakami

first: David

last: Fisher

first: Jun

last: Song


title: Single cell RNA-seq of the human long-term self-renewing neuroepithelial-like stem cell line  SAI2

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: The transcriptome of single long-term self-renewing neuroepithelial-like stem cells (LT-NES) was studied in order to establish a baseline for investigations into modules of synergistically active transcription factors that determine developmental cell subpopulations

overall_design: RNA-seq of 288 single cells

first: Satoshi

last: Okawa

first: Carmen

last: Salto

first: Srikanth

last: Ravichandran

first: Shanzheng

last: Yang

first: Enrique

last: Toledo

first: Ernest

last: Arenas

first: Antonio

last: del Sol


title: Cis-SAGe fusion RNAs in transcription splicing factors knocking-down 293T cells

city: Charlottesville

first: Fujun

last: Qin

state: VA

address: 345 Crispell Dr.

institute: University of Virginia

summary: Total RNA extracted from 15 knocking down treated 293T cells using siRNAs targeting transcription splicing factors and sequenced using Illumina Hiseq PE150 platform to generate RNA sequencing with 150bp in read length. Nearly 50 million raw reads   were yielded from each sample respectively. We used FastQC to confirm the quality of raw fastq sequencing data, and Ericscript software to detect fusion transcripts.

overall_design: Analysis of Cis-SAGe fusion RNAs in the 293T cells with knocking down transcription splicing factors

first: Hui

last: Li


title: Mesothelioma xenografts in nude mice: PBS treated versus pirfenidone treated

city: Helsinki

first: Emmi

last: Joensuu

address: Haartmaninkatu 8

department: Research Programs Unit of the Faculty of Medicine

institute: University of Helsinki

summary:
Background: Malignant mesothelioma is an aggressive cancer with poor prognosis. It is characterized by prominent extracellular matrix, mesenchymal tumor cell phenotypes and chemoresistance. In this study, the ability of pirfenidone to alter mesothelioma cell proliferation and migration as well as mesothelioma tumor microenvironment was evaluated. Pirfenidone is an anti-fibrotic drug used in the treatment of idiopathic pulmonary fibrosis and has also anti-proliferative activities.

Aims: Transcriptional profiling using RNA sequencing of human mesothelioma xenograft tumors treated with PBS or pirfenidone. Aim was to compare extracellular matrix and fibrosis related genes.

Results: Treatment of mice harboring mesothelioma xenografts with pirfenidone alone did not reduce tumor proliferation in vivo. However, pirfenidone modified the tumor microenvironment by reducing the expression of extracellular matrix associated genes. In addition, GREM1 expression was downregulated by pirfenidone in vivo.

Conclusion: By reducing two major upregulated pathways in mesothelioma and by targeting tumor cells and the microenvironment pirfenidone may present a novel anti-fibrotic and anti-cancer adjuvant therapy for mesothelioma.

overall_design: Two condition experiment, PBS treated (CTRL) 3 replicates and pirfenidone treated (PFD) 5 replicates

middle: I

first: Katri

last: Koli


title: H3K27ac profiling of human tracheobronchial epithelial cells during infection with H1N1, H3N2, and H5N1 influenza virus [ChIP-seq]

city: La Jolla

first: Max

last: Chang

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: Human tracheobronchial epithelial (HTBE) cells are considered to serve as a good correlate of influenza virus infection in the human respiratory tract. ChIP-Seq analysis was used to profile histone acetylation (H3K27ac) in HTBE cells at multiple time points in response to infection with influenza A/California/04/09 (H1N1), A/Wyoming/03/03 (H3N2), and A/Vietnam/1203/04 (H5N1) HALo virus. The Influenza A/Vietnam/1203/04 (H5N1) HALo mutant virus is an attenuated H5N1 virus generated from wild-type Influenza A/Vietnam/1203/04 (H5N1) virus as described in Steel, J., et al. J Virol. 2009 Feb; 83(4):1742-53.

overall_design: Human tracheobronchial epithelial cells were infected with H1N1, H3N2, and H5N1 influenza virus at an MOI of 5. H3N2- and H5N1-infected samples were collected in duplicates at 3, 6, 12, and 18 hours post infection for ChIP-Seq analysis. Sample from H1N1-infected cells were collected at 6, 12, 18, and 24 hours. Uninfected controls (mock infection) were also collected at a single time.

first: Matthew

last: Urbanowski

first: Megan

last: Shaw

first: Alex

last: Rialdi

first: Ivan

last: Marazzi

first: Sven

last: Heinz

first: Chris

last: Benner

first: Lars

last: Pache

first: Randy

last: Albrecht

first: Adolfo

last: Garcia-Sastre


title: Alternative splicing Hltf: intron retention-dependent activation of immune tolerance at the feto-maternal interface (RNA-Seq)

city: Lubbock

first: Beverly

last: Chilton

department: Cell Biology & Biochemistry

institute: Texas Tech University HSC

summary:
Purpose: we tested the hypothesis that Hltf deletion in placenta either caused or exacerbated neonatal hypoglycemia via Hif-1α regulation of nutrient transporters.
Methods: Individual samples [1 term placenta/sample x 5 biological replicates for test and control littermate female mice = 10 total samples] were flash frozen and sent to Otogenetics Corp. (Norcross, GA) for RNA-seq assays. Paired-end 100 nucleotide reads were aligned to genomic assembly mm10 and analyzed using the platform provided by DNAnexus, Inc. (Mountain View, CA).
Results: There was no measureable evidence of uteroplacental dysfunction or fetal compromise.
Conclusion: Our study is the first to show only the truncated Hltf isoform is expressed in E18.5 term placenta, and we identified a functional link between alternative splicing of Hltf and immunosuppression at the feto-maternal interface.

overall_design: Placental mRNA profiles of E18.5 term placenta from five wild type control and five Hltf null mouse samples were generated by deep sequencing by Illumina HiSeq2000/2500.

first: Gurvinder

last: Kaur

first: Rebecca

middle: A

last: Helmer

first: Lisa

last: Smith

first: Raul

last: Martinez-Zaguilan

first: Jannette

last: Dufour


title: Alternative splicing Hltf: intron retention-dependent activation of immune tolerance at the feto-maternal interface

type: Methylation profiling by high throughput sequencing


title: Hippocamppal gene expression - C57BL/6 mice exposed to room air or 85% oxygen from P2-P14

city: Birmingham

first: Manimaran

last: Ramani

state: Alabama

address: 1700, 6TH Ave South

department: Pediatrics

institute: University of Alabama at Birmingham

summary: We are reporting the RNA sequence of hippocamppal samples obtained from C57BL/6 mice at P14 following room air or 85% exposure from P2-14

overall_design:
Analysis of hippocamppal genmoic expressions using Next-generation sequencing (NGS  in 85% oxgyen exposed C57BL/6 compared to room air exposed
Mice pups along with their dams were exposed to either 85% oxygen or room air from P2-P14. Genomic expression was analyzed from hippocamppal samples harvested at P14.


title: Alternative splicing Hltf: intron retention-dependent activation of immune tolerance at the feto-maternal interface (Bisulfite-Seq)

summary:
Purpose: Genome-wide methylation analysis was performed to determine whether deleting Hltf altered DNA methylation patterns, and whether differentially methylated regions (DMRs) coincided with changes in transcriptional regulation of Hltf target genes.
Methods: Individual samples [1 term placenta/sample x 3 biological replicates for null and control mice = 6 total samples] were flash frozen prior to DNA isolation and purity assessment. Genomic DNA was sent to Zymo Research (Irvine, CA) for Methyl-MiniSeq Epiquest analysis.
Results: There was no measureable evidence of uteroplacental dysfunction or fetal compromise.
Conclusion: Our study is the first to show Hltf-gene deletion alters the epigenetic landscape of the placenta.

overall_design: Placental DNA methylation profiles of E18.5 term placenta from three wild type control and three Hltf null mouse samples were generated by Methyl-MiniSeq by IluminaHiSeq2000.


title: DNA polymerase η contributes to lagging strand synthesis

city: Göteborg

first: Anders R.

last: Clausen

address: Box 440

institute: University of Gothenburg

summary: DNA polymerase eta (pol eta) is best known for its ability to bypass UV-induced thymine-thymine (T-T) dimers and other bulky DNA lesions, but pol eta also has other cellular roles. Here, we present evidence that pol eta competes with DNA polymerases alpha and delta for the synthesis of the lagging strand genome-wide, where it also shows a preference for T-T in the DNA template. Moreover, we found that the C-terminus of pol eta which contains a PCNA-Interacting Protein motif is required for pol eta to function in lagging strand synthesis. Finally, we provide evidence that a pol η dependent signature is also found to be lagging strand specific in patients with skin cancer. Taken together, these findings provide insight into the physiological role of DNA synthesis by pol eta and have implications for our understanding of how our genome is replicated to avoid mutagenesis, genome instability and cancer.

overall_design: Mapping ribonucleotides in DNA from yeast deficient in rnh201, NER and rev3  by steric gate variants of pols alpha, delta, epsion with HydEn-seq (5' end sequencing of genomic fragments).

first: Katrin

last: Kreisel

first: Martin

middle: K

last: Engqvist

first: Josephine

last: Kalm

first: Liam

last: Thompson

first: Clara

last: Navarrete

first: John

last: McDonald

first: Roger

last: Woodgate

first: Anders


title: Baseline Intrahepatic and Peripheral Innate Immune Responses are Associated with Hepatitis C Virus Eradication in Patients Receiving Direct Acting Antivirals

city: Bethesda

first: Margaret

last: Cam

state: MD

institute: NIH

summary:
Hepatitis C virus (HCV) infection induces interferon stimulated genes (ISGs) and downstream innate immune responses. This study investigated whether baseline and on-treatment differences in these responses predict response versus virological breakthrough during therapy with direct acting antivirals (DAA).
Microarray and nanostring analyses were performed on paired liver biopsies and analyzed using linear mixed models. As biomarkers for peripheral IFN responses, peripheral blood natural killer cells were assessed for pSTAT1 and TRAIL expression and for cytotoxicity.

overall_design: Thirteen HCV genotype 1b-infected patients who had previously failed a course of peginterferon/ribavirin were re-treated with asunaprevir/daclatasvir for 24 weeks. After pre-treatment biopsy, patients were randomized to undergo a second biopsy at week 2 or 4 on-therapy.

first: Hawwa

last: Alao

first: Maggie

first: Marc

last: Ghany


title: Identification and characterization of microRNAs and Piwi-interacting RNAs in cockerels’ sperm by Solexa sequencing

city: Yangling

first: Shengru

last: Wu

address: 22 St.XiNong

department: College of Animal Science and Technology

institute: Northwest A&F University

summary: There have been substantial researches focused on the roles of microRNAs (miRNA) and Piwi-interacting RNAs (piRNA) delivered from mammalian spermatozoa, comparatively little is known about the role of sperm-delivered miRNAs and piRNAs within cockerels’ (breeding cock) sperm. A small RNA library of cockerels’ sperm was constructed using Illumine high-throughput sequencing technology.

overall_design: A small RNA library of cockerels’ sperm was constructed using Illumine high-throughput sequencing technology. Unique sequences with lengths of 18-26 nucleotides were mapped to miRBase 21.0 and unique sequences with lengths of 25-37 nucleotides were mapped to piRNA database. A total of 1,311 miRNAs and 2,448 potential piRNAs were identified. Based on stem-loop qRT-PCR, eight miRNAs were validated.

first: Xiaojun

last: Yang


title: Replacing reprogramming factors with antibodies selected from autocrine antibody libraries

city: LA JOLLA

first: Kristin

last: Baldwin

address: 10550 N. Torrey Pines

department: DNC

institute: TSRI

summary: Identification of antibodies with reprogramming activity from combinatorial libraries

overall_design: Mouse iPSC lines were characterized via RNA sequencing

first: K


title: A developmental program truncates long transcripts to temporally regulate cell signaling

city: Pasadena

first: Angelike

last: Stathopoulos

address: 1200 E. California Blvd

department: Biology and Biological Engineering

institute: California Institute of Technology

summary: Rapid mitotic divisions and a fixed transcription rate limit the maximal length of transcripts in early embryos. Previous studies suggested that transcription of long genes is initiated, but then aborted, in Drosophila embryos as early divisions have short interphases of 15 minutes or less. Here, we identify long genes that are expressed during short nuclear cycles, but as truncated transcripts. The RNA binding protein Sex-lethal is required to specifically support termination of these short transcripts, associating with truncated but not full-length forms. Furthermore, one short product of a truncated transcript for the gene short-gastrulation (sog) relates closely to a previously characterized dominant negative form that maintains TGF-β signaling in the off-state. In summary, our results reveal a developmental program of short transcripts that helps prime the Drosophila embryo, demonstrated by sog, to keep signaling at early stages to a minimum and support proper timing of cell signaling initiation at cellularization.

overall_design: Two separate 3' RNA seq libraries of Drosophila embryos staged at nuclear cycle 13 and nuclear cycle 14

first: Jeremy

last: Sandler

first: Vincent

last: Stepanik

first: Jihyun

last: Irizarry

first: Henry

last: Amrhein


title: Expression analysis of λH1-hESC derived β-like cells

city: Miami

first: Juan

last: Domínguez-Bendala

state: FL

address: 1450 NW 10th Ave Miami

department: Department of Surgery

institute: Diabetes Research Institute, University of Miami, Miller School of Medicine

summary:
Purpose: Pancreatic islet transplantation is an effective cell therapy for type 1 diabetes (T1D), but its clinical application is limited by the shortage of donor pancreata. Among the potential alternatives, the differentiation of human embryonic stem cells (hESc) into insulin-producing β-cells has taken an early lead. However, while the proportion of β-cells obtained through current methods is relatively high, a significant percentage of undefined non-endocrine cell types are still generated. Most importantly, there is the potential for carry-over of non-differentiated cell types that may produce teratomas upon transplantation. In order to address these issues, we sought to modify hESc so that their differentiated progeny could be selectively devoid of tumorigenic cells and enriched for cells of the desired phenotype (in this case, pancreatic β-cells).
Methods: mRNA profiles of λH1-hESC derived β-like cells were developed by mRNA sequencing, in triplicate, using Illumina HiSeq PE Cluster Kit v4 and Illumina HiSeq Flow Cell v4 with 50 nt paired end reads plus dual index reads using the Illumina HiSeq SBS kit v4. Sequence reads that passed quality filters were analyzed at the transcript isoform level following alignment using TopHat v2.1.0 followed by exon and gene level counting using Bioconductor easyRNASeq v 2.4.7.
Conclusions: Our study demonstrates that λH1-hESC derived β-like cells have a transcriptional expression profile similar to ESC derived β-like cells.

overall_design: RNA sequencing data of λH1-hESC derived β-like cells

first: Mirza

last: Fahd Qadir

last: Dominguez-Bendala

first: Ricardo

last: Pastori


title: Longitudinal tracking of whole blood gene-expression in healthy young and old individuals - 2013

status: Public on Dec 13 2018

city: Haifa

first: Ayelet

last: Alpert

address: Techion

country: Israel

institute: Technion

summary: Immune responses generally decline with age. We used multiple ‘omics’ technologies to capture population- and individual- level changes in the human immune system of 135 healthy adult individuals of different ages sampled longitudinally over a nine-year period. We observe a high inter-individual variability in the rates of change of cellular frequencies that correlate with baseline values, allowing identification of steady state levels towards which a cell subset converges and the ordered convergence of multiple cell subsets towards an older adult homeostasis. These form a high dimensional trajectory of immune-aging (IMM-AGE) that describes a person’s immune status better than chronological age. We show the IMM-AGE score predicts all-cause mortality beyond well-established risk factors in the Framingham Heart Study.

overall_design: We analysed whole blood gene-expression transcriptomic changes along the IMM-AGE trajectory representing the dynamics of cellular frequencies.

first: Xuhuai

last: Ji

first: Mark

last: Davis

first: Holden

last: Maecker

first: Shai

last: Shen-Orr


title: Longitudinal tracking of whole blood gene-expression in healthy young and old individuals - 2014


title: Germline variant in SLCO2B1 and response to abiraterone acetate plus prednisone (AA) in new onset metastatic castration-resistant prostate cancer (mCRPC)

city: Salt Lake City

first: Roberto

middle: Henrique

last: Nussenzveig

state: Utah

address: 2000 Circle of Hope

department: Oncology

institute: University of Utah/Huntsman Cancer Institute

summary: There are many treatment options available for men with metastatic castration-resistant prostate cancer (mCRPC). Yet, biomarkers predictive of differential response to treatment are currently available. A recent translational study suggested that SLCO2B1 genotype could predict response to abiraterone acetate (AA) for men with advanced prostate cancer. Here, we investigate whether germline variants in SLCO2B1 are predictive of response to first-line AA in men with new mCRPC. Clinical data and samples were analyzed from a prospective prostate cancer registry at the University of Utah. Genotyping was performed using the Illumina OmniExpress genotyping platform. Primary endpoint was progression-free survival (PFS) on first-line AA in men with mCRPC. We performed a pre-speciﬁed multivariate Cox regression analysis to assess the independent predictive value of rs12422149 and rs1789693 on PFS on AA. Of 401 men with advanced prostate cancer genotyped, 323 were homozygous wild type for rs12422149 (80.5%), 74 were heterozygous (18.5%), and 4 were homozygous variant (1.0%). In a multivariate analysis of 79 men treated with first-line AA for mCRPC, men heterozygous for rs12422149 had significantly improved median PFS compared to the homozygous wild-type group (8.9 months vs. 6.3 months, HR 0.46, 95% CI 0.23-0.94, p=0.03). No significant difference in median PFS was seen by rs1789693 genotype.  In this first clinical validation of translational data reported by Mostaghel and colleagues, germline variant alleles in rs12422149 of SLCO2B1 are common and predict improved response to first-line AA In men with mCRPC.

first: Andrew

last: Hahn

first: David

last: Gill

first: Austin

last: Poole

first: Sara

last: Wilson

first: James

last: Farnham

first: Robert

last: Stephenson

first: Lisa

last: Cannon-Albright

first: Benjamin

middle: L

last: Maughan

first: Neeraj

last: Agarwal


title: CBX8 KO and WT re-expression RNA-seq

city: West Lafayette

first: Emily

last: Dykhuizen

state: IN

address: 201 S. University

department: medicinal chemistry and molecular pharmacology

institute: Purdue University

summary: T98G CBX8 KO and WT re-expression RNA-seq analysis to identify potential CBX8 gene targets

overall_design: T98G CBX8 KO and CBX8 re-expression mRNA in triplicate

first: Katelyn

last: Connelly


title: Cyclin Cyc2 is required for elongation of meiotic micronucleus in Tetrahymena thermophila

city: taiyuan

first: jing

last: xu

state: shanxi

address: wuchen road

institute: shanxi university

summary: Meiosis occurs in all sexually reproducing unicellular and multicellular eukaryotes. Bouquet formation is indispensible for homologous pairing or recombination during meiotic prophase I, but the regulatory mechanism of this process remain largely unknown. Cyclins regulate the precise meiosis progression by activating cyclin-dependent kinases. We therefore investigated the functional contribution of cyclin Cyc2p during bouquet (named crescent in Tetrahymena) formation in Tetrahymena thermophila. As a conjugation specific gene, CYC2 expression is significantly upregulated at 2-4 h after the initiation of conjugation and Cyc2p mainly localized in cytoplasm as well as weakly in the meiotic micronucleus (Mic). CYC2 knockout mutants failed to form elongated crescent structure and aborted meiotic development. Mic DNA double-strand breakage (DSB) decreased in ΔCYC2 cells as shown by γ-H2A.X staining, consistent with the finding that expression level of SPO11, DMC1, and RAD51 decreased in ΔCYC2 cells. However, ΔCYC2 cells failed to form crescent structure when artificial DSBs were induced, indicating that the inability to enter crescent phase was not completely due to the lack of DSBs. The localization of tubulin showed that impaired structure of nuclei and nuclear membrane may contribute to the blocked Mic elongation. This is further supported by the observation that expression levels of two microtubule associated kinesin genes, KIN11 and KIN141, were significantly downregulated in ΔCYC2 cells. Interestingly, scnRNA accumulation seemed intact in ΔCYC2 cells whereas the intensity of the heterochromatin marker H3K23me3 was abnormally increased. Together, these results showed that cyclin Cyc2p is required for micronuclear meiosis by controlling meiotic prophase chromosome breakage and the microtubule movement of nuclei in Tetrahymena.

overall_design: Examination of transcriptional variation associated with deletion of CYC2 gene

first: Jing

last: Xu

first: Wei

last: Wang


title: Longitudinal tracking of whole blood gene-expression in healthy young and old individuals - 2015

first: Ayelet

last: Alpert

first: Xuhuai

last: Ji

first: Mark

last: Davis

first: Holden

last: Maecker


title: The profiling of phospho-ribosomal protein S6 associated RNAs from mouse vomeronasal organ whole cell extract

city: Cambridge

first: Catherine

last: Dulac

address: 16 Divinity Ave

department: Molecular and Cellular Biology

institute: HHMI/Harvard University

summary:
Phospho-ribosome associated RNAs were immunopurified using the antibodies against phospho-S6. The purified RNAs were converted to cDNAs, which were sequenced in Illumina HiSeq platform.
Vomeronasal organs were extracted from male CD-1 animals exposed to either pup cues or fresh bedding.

overall_design: Total of 6 samples, 2 conditions and 3 replicates

first: Yoh

last: Isogai


title: Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [THE1B RACE-Seq]

city: Freiburg

first: Pierre

middle: Daniel

last: Cauchy

state: Baden-Württemberg

address: Breisacher Str. 115

department: Zentrum für Translationale Zellforschung

institute: University Medical Center Freiburg

summary: Long terminal repeat (LTR) elements are wide-spread in the human genome and have the potential to act as promoters and enhancers. Their expression is therefore under tight epigenetic control. We previously reported that a member of the THE1B class of LTR elements in classical Hodgkin Lymphoma (cHL) acted as a promoter for the growth factor receptor gene CSF1R and that expression of this gene is required for tumor survival. However, to which extent and how such elements participate in globally shaping the unique cHL gene expression program is unknown. To address this question we mapped the genome-wide activation of THE1-LTRs in cHL cells using a targeted next generation sequencing approach (RACE-Seq). Integration of these data with global gene expression data from cHL and control B cell lines showed a unique pattern of LTR activation impacting on gene expression, including genes associated with the cHL phenotype. We also show that global LTR activation is induced by strong inflammatory stimuli. Together these results demonstrate that LTR activation provides an additional layer of gene deregulation in classical Hodgkin lymphoma and highlight the potential impact of genome-wide LTR activation in other inflammatory diseases.

overall_design: Sequencing of THE1B 5’ RACE assays in HL, WT NHL, NHL+PMA, NHL+IKK+-dox, NHL+GFP+dox cell lines

last: Edginton-White

first: Salam

last: Assi

first: Sylvia

last: Hartmann

first: Arthur

middle: G

last: Riggs

first: Stephan

last: Mathas

first: Peter

middle: N

last: Cockerill

first: Constanze

last: Bonifer


title: Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [ChIP-Seq]

overall_design: H3K4me3 ChIP-Seq in an HL cell line

first: Benjamin


title: Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [Primary RNA-Seq]

overall_design: RNA-Seq in laser capture microdissected (LCM) tumour (TU) and non tumour cells (NTC) primary HL material from patient samples


title: RNA-seq of Splenic CD4+ T cells and colon epithelial cells from miR-34a-/- and wildtype mice

city: Durham

first: Ergang

state: NC

address: C215, LSRC

department: PCB

institute: Duke University

summary: miR-34a is a known tumor suppressor that targets cell proliferation and apoptosis genes. In this study, we have shown that miR-34a acts as a safeguard for the inflammatory stem cell niche and reparative regeneration by modulating both the immune and epithelial responses to infection and inflammation. We isolated CD4+ T cells and colon epithelial cells from miR-34a-/- and wildtype mice revealed various changes in gene expression.

overall_design: CD4+ T cells and colon epithelial cells are isolated from miR-34a-/- and wildtype mice, each with 3 replicates

first: Lihua

first: Yi

first: Robert

last: Mines

first: Kun

last: Xiang

first: Zhiguo

last: Sun

first: Gaiting

last: Zhou

first: Kai-Yuan

last: Chen

first: Nikolai

last: Rakhilin

first: Shanshan

last: Chao

first: Gaoqi

last: Ye

first: Zhenzhen

last: Wu

first: Huiwen

last: Yan

first: Hong

last: Shen

first: Jeffrey

last: Everitt

first: Pengcheng

last: Bu

first: Xiling


title: Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [RNA-Seq]

first: Pierre

last: Cauchy

overall_design: RNA-Seq in HL, NHL, NHL+PMA cell lines

first: Benjamin

last: Edginton-White

first: Salam

last: Assi

first: Sylvia

last: Hartmann

first: Arthur

last: Riggs

first: Stephan

first: Peter

first: Constanze


title: A platform for generation of chamber specific cardiac tissues and disease modelling

city: Milwaukee

first: Ulrich

last: Broeckel

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary: We report, for the first time, engineering of heteropolar cardiac tissues containing distinct atrial and ventricular ends, and demonstrate their spatially confined responses to serotonin and ranolazine. Uniquely, electrical conditioning for up to 8 months enabled modeling of polygenic left ventricular hypertrophy starting from patient cells.

overall_design: hiPSC-CMs from 3 affected (Left Ventricular Hypertrophy [LVH]) and 3 non-affected donors were sequenced using ThermoFisher's whole transcriptome targeted AmpliSeq assay

first: Yimu

last: Zhao

first: Praful

last: Aggarwal

first: Milica

last: Radisic


title: Thymine DNA Glycosylase as a novel target for melanoma: effect of TDG silencing on gene expression in SK-mel-28 melanoma cells

city: Illkirch-Graffenstaden

first: Guillaume

last: Davidson

address: 1 Rue Laurent Fries

department: Functional Genomics and Cancer

country: France

institute: Institut de Genetique et de biologie moleculaire et cellulaire

summary: Melanoma is an aggressive neoplasm with increasing incidence that is classified by the NCI as a recalcitrant cancer, i.e., a cancer with poor prognosis, lacking progress in diagnosis and treatment. In addition to conventional therapy, melanoma treatment is currently based on targeting the BRAF/MEK/ERK signaling pathway and immune checkpoints. As drug resistance remains a major obstacle to treatment success, advanced therapeutic approaches based on novel targets are still urgently needed. We reasoned that the base excision repair enzyme Thymine DNA Glycosylase (TDG) could be such a target for its dual role in safeguarding the genome and the epigenome, by performing the last of the multiple steps in DNA demethylation.

overall_design: Six samples : cells treated with shTDG and cells treated with shControl both in triplicates.

first: Pietro

last: Mancuso

first: Rossella

last: Tricarico

first: Vikram

last: Bhattacharjee

first: Laura

last: Cosentino

first: Yuwaraj

last: Kadariya

first: Jaroslav

last: Jelinek

first: Emmanuelle

last: Nicolas

first: Margret

last: Einarson

first: Neil

last: Beeharry

first: Karthik

last: Devarajan

first: Richard

last: Katz

first: Dorjbal

last: Dorjsuren

first: Hongmao

last: Sun

first: Anton

last: Simeonov

first: Antonio

last: Giordano

first: Joseph

last: Testa

first: Irwin

first: Lionel

last: Larue

first: Robert

last: Sobol

first: Timothy

last: Yen

first: Alfonso

last: Bellacosa


title: Hippocampal changes in the transcriptome of alpha-synuclein overexpressing mice housed in standard or chronic mild stress environment

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

summary: Using a mouse model overexpressing human SNCA and profiling the striatal transcriptome, we assessed gene-environment interactions to reveal perturbations in gene expression and their modulation through chronic unpredictable mild stress (CUMS) exposure.

overall_design: Using a 2x2 factorial design, we cross-compared a line of transgenic mice overexpressing human SNCA with wildtype animals, and the effects of chronic unpredictable mild stress (CUMS) with standard housing conditions. Employing RNA-seq, we profiled gene expression in the striatum of 6-month-old female animals.

first: Thomas

last: Hentrich


title: Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma

first: Pierre

last: Cauchy

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

overall_design: Refer to individual Series


title: Sufu and Spop cooperate to suppress SHH medulloblastoma tumorigenesis via regulation of Gli2 protein stability [microarray]

city: Toronto

first: Chi-chung

last: Hui

state: Ontario

address: 686 Bay Street. Room 16-9712

department: Developmental & Stem Cell Biology

country: Canada

institute: The Hospital for Sick Children

summary: SUFU alterations are commonly detected in human SHH subgroup of medulloblastoma. Here we profile the gene expression of P13 wildtype and Sufu KO cerebellum, as well as Ptch1 KO MB in biological triplicate.

overall_design: Gene expression of P13 wildtype, Sufu KO, and Ptch1 KO cerebella were profiled by MoGene_1_0_st_v1 array.

first: Wen-Chi

last: Yin


title: Sufu and Spop cooperate to suppress SHH medulloblastoma tumorigenesis via regulation of Gli2 protein stability [RNA-seq]

summary: GLI2 overexpression is a hallmark in SHH subgroup of medulloblastoma (SHH MB). Here we profile the transcriptome of two mouse models of SHH MB expressing high Gli2: SmoM2 overexpression and Sufu;Spop double knockout MB.

overall_design: RNA-Seq of P13 wildtype, SmoM2 OE, and Sufu;Spop DKO mouse MB in biological triplicates.


title: Genome-wide binding of SUDHL4 DLBCL cells

city: New York

first: Katerina

last: Hatzi

state: NY

address: 413 E 69th Street, BB-1462

department: Hematology/Oncology

institute: WCMC

summary: Using ChIP-seq, we identified the genome-wide targets of BCL6 and LSD1 in lymphoma cells SUDHL4 and performed H3K4me1 ChIP-seq in cells treated with control siRNA or siRNA targeted to BCL6.

overall_design: ChIP-seq was performed in lymphoma cells under baseline conditions, treated with control siRNAs or treated with BCL6 targeted siRNAs for 24h.


title: Chromatin accessibility by ATAC in wild type versus knockout GC B cells

summary: Using ATAC-seq, we identified differential chromatin accessibility comparing LSD1 wild type versus knockout GC B cells.

overall_design: To understand how loss of Lsd1 alters chromatin accessibility in GC B cells, we performed ATAC-seq in sorted viable GC B splenocytes (GL7+Fas+B220+) from Lsd1fl/fl (n=2) or Cγ1-Cre;Lsd1fl/fl mice (n=3) ten days after immunization with SRBC.


title: Diabetes Remission Using Glucose-Responsive Insulin-Producing Human α-Cells

city: Kyoto

first: Kenichiro

last: Furuyama

state: Kyoto

address: 53 Shogoinkawahara-cho, Sakyo-ku

department: Life Science Frontiers

institute: CiRA, Kyoto University

summary: Natural and stable cell identity switches, where terminally-differentiated cells convert into different cell-types when stressed, represent a widespread regenerative strategy in animals, yet they are poorly documented in mammals. In mice, some glucagon-producing pancreatic α-cells become insulin expressers upon ablation of insulin-secreting β-cells, promoting diabetes recovery. Whether human islets also display this plasticity for reconstituting β-like cells, especially in diabetic conditions, remains unknown. Here we show that two different islet non-β-cell types, α- and γ–cells, obtained from deceased non-diabetic or diabetic human donors can be lineage-traced and induced to produce insulin and secrete it in response to glucose. When transplanted into diabetic mice, converted human α-cells reverse diabetes and remain producing insulin even after 6 months. Insulin-producing α-cells maintain α-cell markers, as seen by deep transcriptomic and proteomic characterization, and display hypo-immunogenic features when exposed to T-cells derived from diabetic patients. These observations provide conceptual evidence and a molecular framework for a mechanistic understanding of in situ cell plasticity in islet cells, as well as in other organs, as a therapy for degenerative diseases by fostering the highly-regulated intrinsic cell regeneration.

overall_design: Transcriptomic profiles of human pancreatic α-cells that convert  into insulin-producing cells were generated by deep sequencing using Illumina Hi-seq 4000

first: Pedro

last: Herrera


title: High-throughput in vitro DROSHA processing on 38,880 pri-miRNA variants

city: Hong Kong

first: S. Chul

last: Kwon

address: L1-05, Laboratory Block, 21 Sassoon Road, Pokfulam

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: To investigate the precise processing mechanism of pri-miRNA, we prepared 38,880 pri-miRNA variants which contain unique barcode sequences (Fang and Bartel, Mol Cell, 60: 131) and performed high-throughput processing experiments.

overall_design: pri-miRNA pools which contain various sequence or structural elements were processed by recombinant DROSHA and DGCR8 proteins. Using the unique barcode information, cleavage sites per each pri-miRNA variant were identified and quantified.

first: S

first: Jae

last: Woo

first: V

last: Kim


title: WNT ligands control initiation and progression of human papilloma-virus-driven squamous cell carcinoma

city: Zürich

first: Konrad

last: Basler

state: Zürich

address: Winterthurerstrasse 190

department: Institute of Molecular Life Sciences

institute: University of Zürich

summary: Human papilloma virus (HPV)-driven cutaneous squamous cell carcinoma (cSCC) is the most common cancer in immunosuppressed patients. Despite indications suggesting that HPV promotes genomic instability during cSCC development, the molecular pathways underpinning HPV-driven cSCC development remain unknown. We compared the transcriptome of HPV-driven mouse cSCC with normal skin and observed higher amounts of transcripts for Porcupine and WNT ligands in cSCC, suggesting a role for WNT-signaling in cSCC progression. We confirmed increased Porcupine expression in human cSCC samples. Blocking the secretion of WNT-ligands by the Porcupine inhibitor LGK974 significantly diminished initiation and progression of HPV-driven cSCC. Administration of LGK974 to mice with established cSCC resulted in differentiation of cancer cells and significant reduction of the cancer stem cell compartment. Thus, WNT/b-catenin signaling is essential for HPV-driven cSCC initiation and progression as well as for maintaining the cancer stem cell niche. Interference with WNT-secretion may thus represent a promising approach for therapeutic intervention.

overall_design: 4 healthy skin samples, 4 Lgk974 treated murine HPV induced SCC samples, 4 vehicle (DMSO) treated HPV induced SCC samples

first: Dario

last: Zimmerli

first: Maries

last: van den Broek


title: Sufu and Spop cooperate to suppress SHH medulloblastoma tumorigenesis via regulation of Gli2 protein stability [ChIP-seq]

summary: GLI2 overexpression is a hallmark in SHH subgroup of medulloblastoma (SHH MB). Here we identify the targetome of Gli2 in two mouse models of SHH MB: SmoM2 overexpression and Sufu;Spop double knockout MB.

overall_design: Examination of Gli2-bound DNA and H3K27ac- and H3K36me3-modified DNA in P13 Sufu;Spop double knockout and SmoM2 overexpression medulloblastoma in mice


title: ATAC-seq of 8-cell embryo samples

city: Beijing

first: Qi

last: Zhou

address: Datun Road, Chaoyang District

institute: Institute of Zoology,CAS

summary: We hypothesized that LincGET/CARM1 complex activates ICM-specific genes at the 8-cell stage. And we examined chromatin accessibility of these genes by preforming an assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq)

overall_design: The LincGET- or Carm1-overexpressing blastomeres as well as control blastomeres with EGFP overexpressing at the 8-cell stage were collected and peformed for ATAC-seq.

first: Jiaqiang

last: Wang


title: Gene targets and developmental regulation of the honeybee Apis mellifera ftz-f1

city: Alfenas

first: Angel

middle: Roberto

last: Barchuk

state: Minas Gerais

address: Rua Gabriel Monteiro Silva 700, Campus Unifal

department: Cell and Developmental Biology

country: Brazil

institute: Federal University of Alfenas

summary: Ftz-f1 (Fushi tarazu transcription factor 1) is an orphan member of the nuclear hormone receptor superfamily, with one of its transcriptional variant (βFtz-f) being homolog of the vertebrate SF1. Ftz-f1 gene is induced after a 20E pulse, and allows for the expression of down-stream genes in processes leading to major switching in development, like those of metamorphosis. In honeybees, the expression of some genes (e.g. vitellogenin, vg; pro-phenoloxidase, pro-Po; juvenile hormone esterase, jhe) during the last part of pharate-adult development is known to be under hormonal control [increasing juvenile hormone titers (JH) in the presence of declining levels of ecdysteroids], both, in queens and workers. However, despite the USP involvement in the gene expression cascade promoted by JH, it does not seem to be the unique mediator of its activity, and, thus, we are still ignorant of the molecular factors regulating the expression of these genes, at least, during the critical period of pharate-adult development. Here, we show that Amftz-f1 has caste-specific transcription profile in fat bodies during this developmental stage, peaking just at the moment of the resuming of JH titers increase in the presence of low levels of ecdysteroids. Knock-down experiments (by RNAi) showed that the expression of genes essential to adult development (e.g. vg, and cuticular protein genes) depends on ftz-f1. Our results suggest that Amftz-f1 can also be considered a competence factor to the expression of several genes during pharate-adult development, and, thus, as a key actor in one of the last developmental processes leading to caste differentiation in A. mellifera.

overall_design: RNA samples (from pools of 3-5 whole body workers) from knocked-down and control pharate-adults were hybridized in pairs (dsftz-f1/dsGFP) and in dye-swaps (Cy3/Cy5), twice, then, combined in silico.

first: Tathyana

middle: R

last: Mello

first: Aline

last: Aleixo

first: Daniel

last: Pinheiro

first: Francis

last: Nunes

first: Alexandre

last: dos Santos Cristino

first: Márcia

last: Bitondi

first: Zilá

last: Simões


title: Generated different Th cells

status: Public on Dec 12 2018

city: Winston-Salem

first: Yong

last: Lu

address: 575 N. Patterson Ave

department: Dept of Microbiology and Immunology

institute: wake forest school of medicine

summary: Different Th cells were generated in vitro, and then the total RNA was extracted with Rneasy Mini Kit (qiagen).

overall_design: The total RNA of different Th cells was extracted with RNeasy Mini Kit (Qiagen).

first: Gang

last: Xue


title: Sufu and Spop cooperate to suppress SHH medulloblastoma tumorigenesis via regulation of Gli2 protein stability

first: Chi-chung

last: Hui


title: DROSHA complementation experiments using small RNA sequencing

first: S. Chul

last: Kwon

summary: DROSHA complementation experiments were performed to check whether dsRBD of DROSHA recognizes the lower stem of pri-miRNAs and affects miRNA biogenesis.

overall_design: Mature miRNAs were sequenced from HCT116 DROSHA-null cells which had been transfected with wild-type or mutant DROSHA plasmids.

first: S

middle: C

last: Baek

first: Jae

last: Woo

first: V

last: Kim


title: SIRT7-dependent deacetylation of fibrillarin controls H2A methylation and rRNA synthesis during the cell cycle

city: Copenhagen

first: Nicolai

last: Krogh

address: Blegdamsvej 3B

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

summary: Fibrillarin (FBL) is a dual function nucleolar protein which catalyses 2´-O methylation of pre-rRNA and methylation of histone H2A at glutamine 104 (H2AQ104me). The mechanisms that regulate FBL activity are unexplored. Here we show that FBL is acetylated at several lysine residues by the acetyltransferase CBP and deacetylated by SIRT7. While reversible acetylation does not impact FBL-mediated pre-rRNA methylation, hyperacetylation impairs the interaction of FBL with histone H2A and chromatin, thereby compromsing H2AQ104 methylation (H2AQ104me) and rDNA transcription. SIRT7-dependent deacetylation of FBL ensures H2AQ104me and high levels of rRNA synthesis during interphase. At the onset of mitosis, nucleolar disassembly is accompanied by hyperacetylation of FBL, loss of H2AQ104me and repression of Pol I transcription. H2AQ104me and transcriptional activity are restored by overexpression of an acetylation-deficient but not by an acetylation-mimicking FBL mutant. The results reveal that SIRT7-dependent deacetylation impacts nucleolar activity by a FBL-driven circuitry that mediates cell cycle-dependent fluctuation of rDNA transcription.

overall_design: A total of 17 libraires analyzed divided on 6 experimental conditions, where 5 are made in triplicates, and one in duplicates.

first: Aishwarya

last: Iyer-Bierhoff

first: Peter

last: Tessarz

first: Thomas

last: Ruppert

first: Henrik

last: Nielsen

first: Ingrid

last: Grummt