title: A novel IFNα-induced long noncoding RNA, lncMX1-215, negatively regulates immunosuppression by interrupting H3K27 acetylation in head and neck squamous cell carcinoma

first: Hailong

last: Ma

address: Zhizaoju Rd

institute: Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine

summary: Interferon-alpha (IFNα) plays a ciritical role in immune regulation, especially in tumor microenvironment. Our previous study has demonstrated that IFNα promoted immunosuppression formation in head and neck squamous cell carcinoma. To explore the mechanism underlying IFNα-induced immunosuppression, long noncoding RNA (lncRNA) sequece was conduted.   We identified a novel IFNα-induced upregulated lncRNA, lncMX1-215 in HNSCC. It was mainly located in cell nucleus. Ectopic expression of lncMX1-215 markedly inhibited IFNα-induced immunosuppression molecules, programmed cell death 1 ligand 1(PD-L1) and galectin-9 expression, and vice versa. Subsequently, histone deacetylase (HDAC) inhibitors promoted the expression of PD-L1 and galectin-9. There were binding sites of H3K27 acetylation on PD-L1 and galectin-9 promoters. Mechanically, we find that lncMX1-215 directly interacted with GCN5, a known H3K27 acetylase to interrupt its binding to H3K27 acetylation. Clinically, negative correlations between lncMX1-215 and PD-L1, galectin-9 were observed. Finally, overexpression of lncMX1-215 suppressed the proliferation and metastasis capacity in vitro and in vivo in HNSCC.  Our results suggest that lncMX1-215 negatively regulates immunosuppression through interrupting GCN5/H3K27ac in HNSCC and provides novel insights into immune checkpoint blockade treatment.

overall_design: LncRNA sequencing was performed in two HNSCC cell lines, Cal27 and HN30, after treatment with 0,20,200 ng/ml IFNα for 24 h using HiseqXTen platform with two replications.

first: Ma

last: Hailong


title: Vitamin B6 addiction in acute myeloid leukemia

status: Public on Jan 13 2020

city: New York

first: Yu-Jui

last: Ho

state: New York

address: 417 E 68th St

department: Cancer Biology & Genetics Program

country: USA

institute: Memorial Sloan Kettering Cancer Center

type: Expression profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Induction of Recurrent Break Cluster Genes in Neural Progenitor Cells Differentiated from Embryonic Stem Cells In Culture [HTGTS-Seq]

city: Boston

first: Frederick

middle: W

last: Alt

state: MA

address: 1 Blackfan Circle

department: PCMM

institute: Boston Children's Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Our laboratory identified robust recurrent DNA double-strand break (DSB) cluster (“RDC”) genes in mouse neural stem/progenitor cells (NSPCs) by applying the high-throughput, genome-wide, translocation sequencing (HTGTS) method. Genomic alterations of most of the identified RDC-genes have been associated with psychiatric disorders such as autism and schizophrenia and several are altered in brain cancer. The most robust mouse RDCs are all in genes that tend to be very long, actively transcribed and were enhanced after mild inhibition of replication stress. The common transcription and replication characteristics we observe in RDC-genes suggest that frequent RDC DSBs might be generated by collision between transcription and replication processes. However, the underlying mechanism of RDC formation is still unknown.  To elucidate mechanisms that generate and resolve DSBs in these cells, we established an in vitro system of induced neural progenitor cells derived from embryonic stem cells. HTGTS bait-DSBs introduced by CRISPR/Cas9 on three mouse chromosomes identified only 5 RDC-genes in embryonic stem cells and 27 RDC-genes in the neural progenitor cells differentiated from them. All RDC-genes identified in induced neural progenitor cells belonged to the group of genes identified in primary neural and progenitor cells. These results indicate that our in vitro differentiation system is both effective and robust in terms of recapitulating our previous findings and facilitating mechanistic studies.

overall_design: We performed HTGTS-Seq libraries to assess if embryonic stem cells and embronic stem cell-derived neural progenitor cells can harbor recurrent DNA break clusters (RDCs) in vitro when subjected to replication stress.

first: Aseda

last: Tena

first: Yuxiang

last: Zhang

first: Nia

last: Kyritis

first: Anne

last: Devorak

first: Jeffrey

last: Zurita

first: Pei-Chi

last: Wei


title: mRNA expression profiling of Atlantic salmon (Salmo salar) age-at-maturity-associated genes during different developmental stages

city: Helsinki

first: Johanna

last: Kurko

state: --Please select--

address: Biocenter 1, Viikinkaari 9

country: Finland

institute: University of Helsinki

summary: Study revealed new information about molecular functions of the vgll3, akap11 and six6 genes associated with age-at-maturity in Atlantic salmon

overall_design: In the study presented here, expression patterns of three genes associated with age-at-maturity in Atlantic salmon, their paralogs and 205 additional genes were studied in whole hatchery-derived individuals of two embryonic stages, alevin and fry, blood of fry and in different tissues of both hatchery-derived and and wild three-year-old parr.

first: Craig

middle: R

last: Primmer


title: Application of toxicogenomics for the risk assessment of the food contaminant acetamide

city: Research Triangle Park

first: Michael

middle: B.

last: Black

state: North Carolina

address: 100 Capitola Dr., Suite 106

institute: Scitovation, LLC.

summary: Acetamide (CAS 60-35-5) is detected in common foods including milk, eggs, beef, and roasted coffee beans. Chronic rodent bioassays using high doses (≥1000 mg/kg/day) suggest acetamide is a group 2B possible human carcinogen due to the induction of liver tumors. Weight-of-evidence indicates acetamide is not genotoxic, and therefore a threshold response is expected. We used a toxicogenomics approach in Wistar rats gavaged daily for 7 and 28 days to determine the benchmark dose (BMD), and investigate its mode of action from differential gene expression. Two exposure experiements were carried out in succsession.  An initial dose range finding experiment used male Wistar rats gavaged daily for 7 days at 0, 30, 100, 300 and 1000 mg/kd/day.  A second experiment used both male and female Wistar rats exposed for 7 and 28 days to 0, 300,500,750,1000 and 1500 mg/kg/day. No treatment related changes in terminal body weight, clinical chemistry, or histopathology were observed at doses of 30, 100, or 300 mkd. At 1000 mkd, the dose reported to elicit carcinogenesis, liver weights decreased 1.3-fold with the presence of single cell necrosis, hepatocyte vacuolization, and increased mitotic activity consistent with a 4.2 fold increase in the cell proliferation index. Accordingly, plasma ALT and AST were increased 2.0- and 2.2-fold, respectively. RNA-Seq analysis identified 1 differentially expressed gene at 300 mkd, and 2,685 at 1000 mkd (|fold-change| ≥ 1.5 and FDR ≤ 0.05). Down-regulated genes were associated with lipid metabolism while up-regulated genes included cell signaling, immune response, and cell cycle functions. Collectively, these results revealed a no-observable adverse effect level (NOAEL) and no-observed-transcriptional effect level (NOTEL) at 300 mkd, warranting further investigation at doses between 300 and 1000 mkd to identify the benchmark dose (BMD). Functional enrichment indicates perturbation of cell cycle and lipid metabolism, though a more refined dose-response evaluation will be needed to demonstrate dose-dependent effects related to the MOA of acetamide. Funding by the Bill and Melinda Gates Foundation (OPP1142801).

overall_design: Five biological replicates at each exposure for each time point.

first: Rance

last: Nault


title: Array comparative genomic hybridization of Canine Oral Melanoma (COM) archival samples.

city: Legnaro

first: Ginevra

last: Brocca

state: PD

address: Viale dell'Università 16

department: BCA

country: Italy

institute: University of Padova

type: Genome variation profiling by genome tiling array

summary: The aim of this work was to identify the Copy Number Aberrations (CNAs) by high-resolution array Comparative Genomic Hybridization (aCGH) on 19 formalin-fixed, paraffin-embedded (FFPE) samples of treatment-naïve COM.

overall_design: In total, the DNA obtained from 19 COM specimens together with the paired healty tissue present in the same FFPE block were analyzed using a Agilent-025522 SurePrint G3 Canine CGH Microarray 4x180K (GPL10156). Tumor and reference DNA samples were labelled independently with cyanine 5-deoxyuridine triphosphate (dUTP) and cyanine 3-dUTP, respectively, using SureTag Complete DNA Labeling Kit. Oligo aCGH analysis was performed following the manufacturer’s recommendations, using an Oligo aCGH/ChIP-on-chip Hybridization Kit (Agilent Technologies).

first: Massimo

last: Castagnaro


title: Gene expression data from human breast cancer MCF-7 cells treated with siRNA targeting PSF or NONO

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

country: Japan

institute: Saitama Medical University

summary: To examine the role of PSF and NONO in estrogen-dependent breast cancer,  MCF-7 cells were treated with siRNA targeting PSF, NONO or control siRNA (siControl). Microarray analysis revealed PSF- or NONO-regulated genes in MCF-7 cells.

first: Yuichi

last: Mitobe

first: Kaori

last: Iino

first: Kuniko

last: Horie-Inoue

first: Satoshi

last: Inoue


title: Molecular signatures of dengue virus-specific IL-10/IFN-γ co-producing CD4 T cells and their association with severe dengue disease

city: Seattle

first: Yuan

last: Tian

state: WA

address: 1100 Fairview Ave N

institute: Fred Hutchinson Cancer Research Center

summary: Dengue virus (DENV) infection is associated with a range of clinical manifestations, from self-limiting dengue fever (DF) to life-threatening dengue hemorrhagic fever (DHF) and dengue shock syndrome (DSS). Although DENV-specific CD4 T cells are capable of producing inflammatory cytokines and can acquire cytotoxic functions in previously DENV-exposed individuals, much less is known related to DENV-specific CD4 T cells during acute DENV infection and disease. In this study, we set out to characterize the immune signatures of DENV-specific CD4 T cells during acute infection and investigate whether DENV-specific CD4 T cell response differs between DF and DHF. Previous studies suggest that increased IL-10 level in the blood is associated with severe dengue disease. Here we show evidence of DENV-specific IL-10-producing CD4 T cells during acute DENV infection. More specifically, an IL-10+IFN-γ+ double positive (DP) CD4 T cell population was prominent in acute hospitalized DENV cases but disappeared at the convalescent stage. RNA-sequencing analysis revealed that these cells were associated with gene signatures that marginally overlapped with previously identified signatures of cytotoxic CD4 T cells and type 1 regulatory T (Tr1)-like cells. However, the majority of the genes differentially expressed by DP cells were not related to cytotoxic CD4 T cells or Tr1-like cells. These genes include IL-21, IL-22, CD86, CD109, and CCR1, which are involved in T cell activation, function, cytokine signaling, and migration. Notably, the magnitude of DP cell response was higher in DHF than DF, whereas the gene expression profile of DP cells was similar between DF and DHF. Finally, our data show that DENV-specific DP cells are largely homogeneous based on the expression of 31 selected markers. Overall, this study reveals unique phenotypes of virus-specific IL-10/IFN-γ co-producing CD4 cells and indicates that the quantity but not quality of these cells may be positively correlated with dengue disease severity.

overall_design: RNA-sequencing of sorted dengue virus epitopes-stimulated IL-10-IFN-γ-, IL-10+IFN-γ-, IL-10-IFN-γ+, and IL-10+IFN-γ+ CD4 T cells from cryopreserved PBMC of 10 dengue fever (DF) and 10 dengue hemorrhagic fever (DHF) patients

first: Grégory

last: Seumois

first: Sara

last: Herrera de la Mata

first: Pandurangan

last: Vijayanand

first: Bjoern

last: Peters

first: Daniela

last: Weiskopf

first: Alessandro

last: Sette


title: Transcriptome Sequencing of Solid Fermentation under Different Induced Carbon Sources II

city: zhengzhou

first: Li

last: Xudong

state: Henan

address: No. 1, Jianshe East Road, Erqi District

country: China

institute: The First Affiliated Hospital of Zhengzhou University

summary:
Transcriptomic profiling and real-time quantitative reverse transcription-PCR analyses revealed that TP05746 dynamically regulated the expression of genes encoding major PBDEs. Furthermore, in vitro binding experiments confirmed that TP05746 directly bound to the promoter regions of these major enzyme genes.
Transcription factors mediated the regulation of plant-biomass-degrading enzyme (PBDE) gene expression in Talaromyces pinophilus.

overall_design:
TPKu70 was constructed by knocking out TpKu70 gene in strain 1-95
MuTP05746 was constructed by knocking out TP05746 gene in the TPKu70

first: Shuai

last: Zhao

first: Ting

last: Zhang


title: Printer emitted particles (PEPs) exposed rat lung miRNA expression profiling

city: Morgatown

first: Nancy

middle: Lan

last: Guo

state: WV

address: 2816 Health Sciences Center

department: Occupational and Environmental Health Sciences

institute: West Virginia University

summary:
Printer emitted particles (PEPs)-induced cardiopulmonary adverse effects and health risks and the underlying mechanisms are unknown. The aim of this study was to perform genome-wide mRNA profiling in rat blood to identify non-invasive blood based biomarkers for medical and occupational surveillance.
The rats were exposed to printer emitted particles PEPs (exposed) and high efficiency particulate air (HEPA) filtered air (control). Animals were sacrificed on 1, 5, 9,  and 21 days for lung tissue collection.

middle: L


title: Printer emitted particles (PEPs) exposed rat blood miRNA expression profiling

summary:
Printer emitted particles (PEPs)-induced cardiopulmonary adverse effects and health risks and the underlying mechanisms are unknown. The aim of this study was to perform genome-wide mRNA profiling in rat blood to identify non-invasive blood based biomarkers for medical and occupational surveillance.
The rats were exposed to printer emitted particles PEPs (exposed) and high efficiency particulate air (HEPA) filtered air (control). Animals were sacrificed on 1, 5, 9, 13, 17 and 21 days for blood collection.


title: Gastric squamous-columnar junction contains a large pool of cancer-prone immature osteopontin responsive Lgr5-CD44+ cells

city: Ithaca

first: Alexander

middle: Yu.

last: Nikitin

state: NY

address: 618 Tower Road T6 018A VRT

institute: Cornell Universty

summary: We report the gene expression profiles of gastric squamous-columnar junction cancer derived from the mice with conditionally inactivation of Trp53 and Rb1 genes in Lgr5+ cells

overall_design: Examination of gene expression profiles between 5 cancer samples and 3 normal control tissues

middle: Y

first: Dah-Jiun

last: Fu


title: Printer emitted particles (PEPs) exposed rat expression profiling

platform_organism:
Rattus norvegicus
synthetic construct


title: Printer emitted particles (PEPs) exposed rat lung mRNA expression profiling


title: Printer emitted particles (PEPs) exposed rat blood mRNA expression profiling


title: Treatment-induced tumor dormancy through YAP-mediated transcriptional reprogramming of the apoptotic pathway

first: Kari

last: Kurppa

address: 450 Brookline Ave

institute: Dana-Farber Cancer Institute


title: PRC1 facilitates stage-specific enhancer-promoter contacts during Drosophila development

status: Public on Jan 12 2020

city: Montpellier

first: Vincent

last: Loubiere

state: FRANCE

address: 141 rue de la Cardonille

department: Institute of Human Genetics

country: France

institute: UMR9002; CNRS-UM

summary: Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) are highly conserved epigenetic factors that collaborate at multiple levels to maintain their target genes in a repressed state. However, recent reports suggest that PRC1 binds a subset of active promoters and enhancers devoid of the PRC2-mediated H3K27me3 repressive mark in both Drosophila and mammals. Here, we characterize the 3D epigenome of Drosophila Eye-antennal imaginal discs (EDs) and identify a large set of PRC1-bound promoters and enhancers that show preferential interactions in 3D. These PRC1-centered contacts are generally not pre-formed in embryos and coincide with increased PRC1 binding at the larval stage, a concomitant increase in expression during development and mis-regulation in PRC1 mutants. A detailed analysis of the dachshund locus indicates that PRC1-anchored chromatin loops are not only repressive structures, but might also be required for gene activation. Finally, a meta-analysis of RING1B binding profiles and 3D contacts during mouse neural differentiation suggests that this function might be conserved in mammals. These data suggest that, in addition to its known function in gene silencing, PRC1 binding to enhancers and promoters favors stage-specific 3D contacts to facilitate transcription of key developmental genes.

overall_design:
Characterization of the 3D epigenetic landscape of the Polycomb Repressive Complex 1 (PRC1) during Drosophila development using ChIP-Seq, RNA-Seq and Hi-C methods.

Please note that the *merge* processed files were generated by merging all the replicates and are linked to the corresponding rep1 sample records.

first: V

first: G

last: Papadopoulos

first: Q

last: Szabo

first: A-M

middle: M

last: Martinez

last: Cavalli


title: N6-methyladenosine (m6A) profiling of ovarian cancer tissues

city: CHICAGO

first: Zijie

state: IL

department: Chemistry

institute: University of Chicago

summary: We developed RADAR , a method for detecting differential methylated loci in MeRIP-seq data. RADAR uses a flexible model to accommodate increased noise due to RNA immunoprecipitation and are compatible with complex study design. RADAR enabled accurate identification of altered methylation sites in patient  samples where covariates need to be accounted for. We use the m6A-profiling of ovarian cancer data as an example data set to benchmart the performance of RADAR and a few alternative methods.

overall_design: Six omental tumor tissues were collected from newly diagnosed patients with advanced, metastatic high-grade serous ovarian cancer. Seven normal fallopian tube tissues were collected from patients with benign gynecological conditions. Total RNA was extracted from the tissue by TRIzol followed by fragmentation with Bioruptor ultrasonicator. m6A-immunoprecipitation were performed using EpiMark N6-Methyladenosine enrichment kit (NEB cat. E1610S). Takara Pico-Input Strand-Specific Total RNA-seq for Illumina was used to construct library from total RNA where ribosome-derived cDNA was removed before final library amplification. The libraries were sequenced by the NextSeq 500 platform at PE37 mode.

first: Agnieszka

last: Chryplewicz

first: Mark

last: Eckert

first: Chuan

last: He


title: Androgen Receptor Degraders Overcome Common Resistance Mechanisms Developed During Prostate Cancer Treatment

city: Ann Arbor

first: Steven

last: Kregel

state: MI

address: 1500 E. Medical Center Drive, Room 5320 RCC

department: MCTP

institute: University of Michigan

summary: RNA-sequencing of VCaP and LNCaP, LNCaP-EnzR, or LNCaP AR-V7 overexpressing prostate cancer cell lines treated with AR degrader ARD-61.

overall_design: VCaP cells treated with 100nM ARD-61 or DMSO control for 6 hours, and LNCaP, LNCaP-EnzR, or LNCaP AR-V7 cells treated with 100nM ARD-61b for 24 hours

first: Arul

last: Chinnaiyan


title: INCREASED HEAT SHOCK PROTEIN 70 EXPRESSION BY CM-695 ASSOCIATES WITH STRONG ANTITROMBOTIC EFFECT WITHOUT INCREASING BLEEDING

city: Pamplona

first: Jose

last: Hermida

address: Pio XII 55

country: Spain

institute: CIMA

summary:
BACKGROUND
Antithrombotic medications target coagulation factors. Their use is associated with an increased bleeding risk. Safer drugs are needed. We described that the heat shock protein 70 (Hsp70) exhibits antithrombotic properties that do not influence bleeding.
OBJECTIVES
By using murine models, we want to test the hypothesis that overexpressing Hsp70 with CM-695, a dual inhibitor of HDAC6 and phosphodiesterase 9, protects against thrombosis while leaves bleeding tendency unaltered.
METHODS
CM-695 was used to induce Hsp70 overexpression. Hsp70 overexpressing mice were submitted to three thrombosis-triggering procedures. The ferric chloride carotid artery model was used to compare the antithrombotic role of CM-695 and rivaroxaban, a direct oral anticoagulant. The mouse tail transection model was used to compare the bleeding tendency upon CM-695 or rivaroxaban administration.
RESULTS
Intraperitoneal (i.p.) 20 mg/kg CM-695 increased Hsp70 expression markedly in the murine aortic tissue. This treatment delayed thrombosis in the collagen/epinephrine [P=0.04 (Log-Rank test), n=10], Rose Bengal/laser [median vessel occlusion time (OT): 58.6 vs. 39.0 minutes (min) in the control group (CG), P=0.008, n≥10] and ferric chloride (OT: 14.7 vs. 9.2 min in the CG, P=0.032, n≥10) models. I.p. 80 mg/kg CM-695 (n≥9) and intravenous 3 mg/kg rivaroxaban (n≥8) significantly delayed thrombosis. CM-695 did not induce bleeding [median bleeding time (BT): 8.5 vs. 7.5 min in the CG, n≥10]. However, this was dramatically increased by rivaroxaban (BT: 30.0 vs. 13.7 min in the CG, P=0.001, n=10).
CONCLUSIONS
CM-695 is a new antithrombotic drug devoid of bleeding risk that may be envisioned as a useful clinical tool.

overall_design: Two groups of 6 mice each were i.p. administered CM-695 (80 mg/kg twice: two and one hour before sacrifice) or vehicle (saline solution once before sacrifice).

first: Mikel

last: Allende

first: Elizabeth

last: Guruceaga

first: Eva

last: Molina

first: Ramón

last: Lecumberri

first: Julen

last: Oyarzabal


title: A microRNA signature of toxic extrasynaptic N-methyl-D-aspartate (NMDA) receptor signaling

city: Heidelberg

first: Carlos

last: Bas Orth

address: Im Neuenheimer Feld 307

department: Anatomy and Cell Biology

country: Germany

institute: Ruprecht-Karls-University Heidelberg

summary: The cellular consequences of N-Methyl-D-Aspartate receptor (NMDAR) stimulation depend on the receptors’ subcellular localization. Synaptic NMDARs promote plasticity and survival whereas extrasynaptic NMDARs mediate excitotoxicity and contribute to cell death in neurodegenerative diseases. The mechanisms that couple activation of extrasynaptic NMDARs to cell death remain incompletely understood. We here show that activation of extrasynaptic NMDARs by bath application of NMDA or L-glutamate leads to the upregulation of a group of 19 microRNAs in cultured mouse hippocampal neurons. In contrast, none of these microRNAs is induced upon stimulation of synaptic activity. Increased microRNA expression depends on the pri-miRNA processing enzyme Drosha, but not on de novo gene transcription. These findings suggest that toxic NMDAR signaling involves changes in the expression levels of particular microRNAs.

overall_design: Changes in microRNA expression were measured in primary mouse hippocampal neurons in vitro 4 hours after induction of synaptic activity with 50µM bicuculline and 4 hours after activation of NMDA-receptors with 20µM NMDA. Three independent experiments were performed.

last: Bas-Orth

first: Hilmar

last: Bading


title: miR363-3p Mediates Maintenance and Chemoresistance of Breast Cancer Stem Cells

city: Lausanne

first: Nicolas

last: Mermod

address: Station 6, EPFL

department: Lab of Molecular Biotechnology

country: Switzerland

institute: University of Lausanne

summary:
There is increasing evidence that cancer recurrence and resistance to chemotherapy are linked to a subset of cancer stem cells. However, detecting these cells specifically and targeting them therapeutically remain challenging. As microRNAs (miRNAs) are emerging as key players in cancer biology, we set up to identify miRNAs involved in chemoresistance of breast cancer stem cells. In this study, we enriched populations of chemoresistant cancer stem cells from breast cancer and non-transformed breast cell lines using mammospheres. These mammospheres were treated or not with two chemoreagents, and we profiled surviving cells using miRNA microarray analysis. Comparison of the profiles from treated and untreated mammospheres as well as control and cancer cells yielded a six-miRNAs signature specific for chemoresistant stem cell-enriched subpopulations. From this signature miR-363-3p was found to be most highly overexpressed in various breast cancer cell lines and derived cancer stem cell-enriched populations, whereas non-tumorigenic cells had low levels. Inhibition of miR-363-3p was found to decrease cancer stem cell maintenance and tumorigenicity in vitro. Consistently, miR-363-3p downregulation decreased tumor growth and metastatization by human tumor cells transplanted in mice. Finally, miR363-3p levels in the sera of 38 breast cancer patients enrolled in a neoadjuvant trial correlated well with the response to the chemotherapeutic treatments. Altogether, miR363-3p was identified as a mediator of the breast cancer stem cell phenotype, and it may provide a predictor of the response to chemotherapy from a simple blood test, as well as a potential therapeutic approach for cancer stem cell targeting.
This data set aims at identifying differentially expressed miRNAs in chemoresistant mammospheres, by the profiling of miRNA in MCF7 breast cancer cell-derived mammospheres selected to be resistant to 5 Fluorouracil (5FU) or Paclitaxel, as compared to unselected MCF7 mammospheres.

overall_design: miRNA expression was measured in eight samples. There are two untreated samples of normal breast cells (MCF10A) grown as mammospheres, two untreated samples of the breast cancer cell line MCF7 grown as mammospheres,  two untreated samples of the breast cancer cell line MDA grown as mammospheres, and two additional samples from cell line MCF7 grown as mammospheres and treated with 5FU or Paclitaxel.

first: Stéphanie

last: Renaud


title: Next Generation Sequencing of miRNome of G-CSF treated huCD34+ HSPCs

city: Leipzig

first: Gerhard

last: Behre

address: Johannisallee 32A

department: Division of Hematology and Oncology

institute: Leipzig University Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are a class of small non coding RNAs (ncRNAs) with 19-25 nucleotides in length, which can inhibit the translation or induce the destabilization and/or degradation of their mRNA targets, usually by binding in an incomplete manner to the 3`untranslated region (3`UTR) of their respective targets. We were interested in miRNAs that are regulated during G-CSF induced myeloid differentiation.

overall_design: Examination of miRNA expression patterns upon G-CSF administration on huCD34+ HSPCs. NGS was performed out of 3 independent experiments.

first: Jens-Uwe

last: Hartmann


title: Genome-wide methylation analysis of osteosarcoma and Ewing sarcoma using Infinium HumanMethylation 450 BeadChip

city: Chuo-ku

first: Satoshi

last: Yamashita

state: Tokyo

address: Tsukiji 5-1-1

institute: National Cancer Center Research Institute

type: Methylation profiling by genome tiling array

summary: DNA methylation in osteosarcoma and Ewing sarcoma

overall_design: A picture of epigenetic alterations in osteosarcoma and Ewing sarcoma was characterized.

first: Naofumi

last: Asano

first: Hideyuki

last: Takeshima

first: Eisuke

last: Kobayashi

first: Akira

last: Kawai

first: Tadashi

last: Kondo

first: Toshikazu

last: Ushijima


title: Identification of miR-143 mRNA-targets by AGO-RIP in the myeloid cell line K562

summary: MiR-143 is a miRNA commonly found to  be downregulated in a variety of cancers. The goal of this study is the identifacation of miR-143 target mRNAs by next generation sequencing (NGS) in myeloid cells after overxpression of miR-143.

overall_design: We lentiviraly overexpressed miR-143 in the myeloid cell line K562. After selection of positive cells we isolated RNAs associated with the RNA induced silencing complex (RISC) by immunoprecipitation of AGO2. Isolated RNA of 3 independent experiments was subjected to next generation sequencing.

first: J-U


title: Differential gene expression between feminized C. elegans male and female germlines

city: New York

first: Sarah

middle: Elizabeth

last: Albritton

address: 100 Washington Square East

department: Biology

institute: New York University

summary: With the aim to determine the extent of germline feminization in feminized male worms, we performed differential gene expression profiling of isolated gonads and whole worms between fog-1(q253) XO males and XX females.

overall_design: mRNA-seq data sets were generated from fog-1(q253) XO males and XX females grown at the restrictive temperature. Both gonadal and whole worm YA samples were obtained.

first: Tamara

last: Mikeladze-Dvali

first: Sevinc

last: Ercan

middle: E


title: Gene expression-based, individualized outcome prediction for osteoporosis with vertebral fracture

city: Hong Kong

first: Mengge

last: Sun

address: 21 Sassoon Road

country: Hong Kong

institute: The University of Hong Kong

summary: This study aims to identify specific miRNAs profiles in osteoporotic patients with and without vertebral fractures. MiRNAs array analysis was performed on the plasma samples including a pool of 6 miRNA samples from osteoporotic patients with vertebral fractures, a pool of 6 miRNA samples from osteoporotic patients without fracture and another pool of 6 miRNA samples from nonosteoporotic patients to identify regulated miRNAs in the plasma.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: In the study presented here, a pool of 6 miRNA samples from osteoporotic patients with vertebral fractures, a pool of 6 miRNA samples from osteoporotic patients without fracture and another pool of 6 miRNA samples from nonosteoporotic patients were analyzed to identify regulated miRNAs in the plasma.


title: Mouse ovarian cancer models recapitulate the human tumor microenvironment and patient response to treatment

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

country: United Kingdom

institute: Queen Mary University of London

summary: Although there are many prospective targets in the tumor microenvironment (TME) of high-grade serous ovarian cancer (HGSOC), pre-clinical testing is challenging especially as there is limited information on the murine TME. Here, we have characterized the TME of six orthotopic, transplantable syngeneic HGSOC lines established from genetic models and compared these to patient biopsies. This analysis identified significant correlations between the transcriptome, host cell infiltrates, immune response, matrisome, vasculature and tissue modulus of mouse and human TMEs, with several stromal and malignant cell targets in common. However, each model showed distinct differences and potential vulnerabilities that enabled us to predict response to chemotherapy and an anti-IL-6 antibody. The transcriptional profiles of the mouse tumors that differed in chemotherapy response were able to classify chemotherapy-sensitive and -refractory patient tumors. These models provide useful pre-clinical tools and may help identify subgroups of HGSOC patients most likely to respond to specific therapies.

overall_design: RNA sequencing on whole tumours from: A) six transplantable syngeneic murine HGSOC lines (HGS1, n =3 ; HGS2, n=4; HGS3, n = 4; HGS4, n=5 ; 60577, n=5; 30200, n =4)  along with tumours from a genetically modified mouse model (n = 3) and control non-diseased omental tissue (C57Bl/6, n=5 ; FVB, n=4) and B) human HGSOC omental metastasis tumours (n=5) and uninvolved omenta (n=3).

first: Chiara

last: Berlato

first: Ganga

last: Gopinathan

first: Owen

last: Heath

first: Frances

last: Balkwill


title: Fidelity of translation initiation is required for coordinated respiratory complex assembly

city: Perth

first: Stefan

middle: J

last: Siira

state: Western Australia

address: 15 Hospital Ave, Nedlands

department: Precision Health

country: Australia

institute: The Kids Research Institute Australia

summary: Mammalian mitochondrial ribosomes are unique molecular machines that translate 11 leaderless mRNAs. To date it is not clear how mitoribosomes recognize and initiate translation in the absence of untranslated regions in the mitochondrial mRNAs. Translation initiation in mitochondria shares similarities with prokaryotic systems, such as the formation of a ternary complex of fMet-tRNAMet, mRNA and the 28S subunit, but differs in the requirements for initiation factors. Mitochondria have two initiation factors, MTIF2 that closes the decoding centre and stabilizes the binding of the fMet-tRNAMet to the leaderless mRNAs, and MTIF3 whose role is not clear. We knocked out Mtif3 in mice and show that this protein is essential for embryo development and heart- and skeletal muscle-specific loss of MTIF3 causes premature death. We identify increased but uncoordinated mitochondrial protein synthesis in mice lacking MTIF3 that results in loss of specific respiratory complexes. Therefore, we show that coordinated assembly of OXPHOS complexes requires stoichiometric levels of nuclear and mitochondrially-encoded protein subunits in vivo. Our ribosome profiling and transcriptomic analyses show that MTIF3 is required for recognition and regulation of translation initiation of mitochondrial mRNAs, but not dissociation of the ribosome subunits.

overall_design: Total RNA was isolated from heart tissue from 25 week old control (Mtif3loxP/loxP) and Mtif3 knockout mice (Mtif3loxP/loxP, +/Ckmm), and TruSeq libraries produced, sequenced and analysed for differential expression. Sucrose gradient fractions of mitochondrial RNA corresponding to small and large subunit, as well as assembled ribosomes, was isolated from heart tissue from 25 week old control (Mtif3loxP/loxP) and Mtif3 knockout mice (Mtif3loxP/loxP, +/Ckmm), and ribosome profiling libraries produced and sequenced.

first: Danielle

last: Rudler

first: Laetitia

last: Hughes

first: Kara

last: Perks

first: Tara

last: Richman

first: Irina

last: Kuznetsova

first: Judith

middle: A

last: Ermer

first: Laila

middle: N

last: Abudulai

first: Anne-Marie

last: Shearwood

first: Helena

last: Viola

first: Livia

middle: C

last: Hool

first: Oliver

last: Rackham

first: Aleksandra

last: Filipovska


title: Altered mRNA expression in sika deer skeletal muscle with age

status: Public on Jan 11 2020

city: Changchun

first: Boyin

last: Jia

state: Jilin

address: 2888 Xincheng Street

department: College of Animal Science and Technology

institute: Jilin Agricultural University

summary: Studies of the gene expression profiles associated with the postnatal late growth, development and aging of skeletal muscle are lacking in sika deer. To understand the molecular mechanisms of the growth and development of sika deer skeletal muscle, we used de novo RNA-seq analyses to determine the diﬀerential expression of unigenes from skeletal muscle tissues at 1, 3, 5, and 10-year-old in sika deer. A total of 51716 unigenes were identified based on four mRNA libraries. 2044 unigenes were differentially expressed between adolescence and juvenile sika deer, 1946 unigenes were differentially expressed between adult and adolescence sika deer, and 2209 unigenes were differentially expressed between aged and adult sika deer. GO and KEGG analyses showed that DE unigenes were mainly related to energy and substance metabolism, processes that are closely associate with growth, development and aging of skeletal muscle. We also constructed mRNA-mRNA interaction networks related to growth, development and aging of skeletal muscle. The results showed that Myh1, Myh2, Myh7, ACTN3 etc. may play important roles in muscle growth and development, and WWP1, DEK, UCP3, FUS etc. may have key roles in muscle aging. In this study, we determined the dynamic unigenes transcriptome in muscle tissue for the first time in sika deer. The age-dependent unigenes identified will offer insights into the molecular mechanism underlying muscle development, growth and maintenance and also provide valuable information for sika deer genetic breeding.

overall_design: The gene expression profiles of skeletal muscle tissues at 1, 3, 5, and 10-year-old in sika deer were generated by Illumina HiSeq2500 sequencing

first: Dongdong

last: Liu

first: Fuhe

last: Yang


title: Joint Location-Specific JAK-STAT Signaling in Rheumatoid Arthritis Fibroblast-like Synoviocytes

city: La Jolla

first: Gary

middle: S

last: Firestein

state: CA

address: 9500 Gilman Dr MC0656

institute: UC San Diego

summary: Rheumatoid arthritis (RA) fibroblast‐like synoviocytes (FLS) derived from hip and knee have distinctive DNA methylation and transcriptome patterns in interleukin (IL)‐6 signaling and Janus kinase (JAK)–signal transducers and activators of transcription (STAT) pathways. To determine the functional effects of these joint‐specific signatures, we evaluated how RA hip and knee FLS differ in their response to IL‐6.Hip or knee RA FLS were obtained after arthroplasty. Previously published datasets on epigenetic landscape of FLS were mined to identify joint‐specific IL‐6–related epigenomic differences. RNA sequencing was performed on five RA hip and five knee FLS treated with or without IL‐6. Differential gene expression was determined using edgeR software. STAT3 phosphorylation was measured using bead assays. Sensitivity to tofacitinib was evaluated by measuring CCL2 inhibition using quantitative polymerase chain reaction. Assay for Transposase‐Accessible Chromatin sequencing and histone chromatin immunoprecipitation sequencing datasets from RA FLS were analyzed to identify epigenomic differences between hip and knee. Differential chromatin accessibility was associated with IL‐6, IL‐6R, and JAK1 genes. H3K27ac was also differentially marked at other JAK‐STAT–related genes, including STAT3‐STAT5A region. Principal component analysis of RNA sequencing data confirmed segregation between RA hip and knee FLS under basal conditions, that persisted following IL‐6 treatment. STAT3 phosphorylation after IL‐6 was significantly higher in knee than hip FLS and was highly correlated with JAK1 protein levels. Knee FLS were less sensitive to the JAK inhibitor tofacitinib than hip FLS. RA hip and knee FLS have distinct transcriptomes, epigenetic marks, and STAT3 activation patterns in the IL‐6 pathway. These joint‐specific differences might contribute to a differential clinical response in individual joints to targeted therapies such as JAK inhibitors.

overall_design: Total RNA-seq from IL-6-stimulated knee and hip rheumatoid arthritis FLS

first: D

last: Hammaker

first: G

last: Nygaard

first: A

last: Kuhs

first: R

last: Ai

last: Boyle

first: W

last: Wang


title: Nuclear peripheral positioning of heterochromatin by Amo1NUPL2 suppresses nucleosome turnover to promote epigenetic inheritance [ChIP-seq]

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: NCI bldg 37 Rm 6068 9000 Rockville Pike

department: LBMB

institute: NCI

summary: Occupancy profiling of GFP-tagged Rix1 protein in fission yeast.

overall_design: Mapping of GFP-Rix1 in WT and swi6-115 muatnt S. pombe strains with and without B-box deletion.

first: Sahana

last: Holla

first: H

middle: D

last: Folco

first: Jothy

last: Dhakshnamoorthy

first: Vanivilasini

last: Balachandran

first: Hua

last: Xiao

first: David

last: Wheeler

first: Martin

last: Zofall

middle: I


title: Altered miRNA expression in sika deer skeletal muscle with age

first: Boyin

last: Jia

summary: Studies of the miRNA expression profiles associated with the postnatal late growth, development and aging of skeletal muscle are lacking in sika deer. To understand the molecular mechanisms of the growth and development of sika deer skeletal muscle, we used de novo RNA-seq analyses to determine the diﬀerential expression of miRNAs from skeletal muscle tissues at 1, 3, 5, and 10-year-old in sika deer. A total of 171 known miRNAs and 60 novel miRNAs were identified based on four small RNA libraries. 11 miRNAs were differentially expressed between adolescence and juvenile sika deer, 4 miRNAs were differentially expressed between adult and adolescence sika deer, and 1 miRNAs were differentially expressed between aged and adult sika deer. GO and KEGG analyses showed that miRNA were mainly related to energy and substance metabolism, processes that are closely associate with growth, development and aging of skeletal muscle. We also constructed mRNA-mRNA and miRNA-mRNA interaction networks related to growth, development and aging of skeletal muscle. The results showed that miR-133a, miR-133c, miR-192, miR-151-3p etc. may play important roles in muscle growth and development, and miR-17-5p, miR-378b, miR-199a-5p, miR-7 etc. may have key roles in muscle aging. In this study, we determined the dynamic miRNA in muscle tissue for the first time in sika deer. The age-dependent miRNAs identified will offer insights into the molecular mechanism underlying muscle development, growth and maintenance and also provide valuable information for sika deer genetic breeding.

overall_design: The miRNA expression profiles of skeletal muscle tissues at 1, 3, 5, and 10-year-old in sika deer were generated by Illumina HiSeq2500 sequencing

last: Liu


title: Nuclear peripheral positioning of heterochromatin by Amo1NUPL2 suppresses nucleosome turnover to promote epigenetic inheritance [ChIP-chip_C300]

type: Genome binding/occupancy profiling by genome tiling array

summary:
Occupancy profiling of GFP-tagged Rix1, Las1, Ipi1, Crb3 proteins in fission yeast.
Occupancy profiling of lysine 9 trimethylated histone H3 in fission yeast.

overall_design: Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of  GFP-tagged proteins or K9-trimethylated histones from asynchronous culture of fission yeast.


title: Altered expression in sika deer skeletal muscle with age

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

overall_design: Refer to individual Series


title: Nuclear peripheral positioning of heterochromatin by Amo1NUPL2 suppresses nucleosome turnover to promote epigenetic inheritance [ChIP-chip_C50]

summary: Occupancy profiling of FLAG-tagged H3 in fission yeast.

overall_design: Agilent 60mer array was used to analyze DNA recovered by immunoprecipitation of  FLAG-tagged histone H3 from nucleosome turnover experiments.


title: Gene expression and chromatin accessibility of iLSCs vs iBlasts cells

first: Josephine

last: Wesely

address: 1470 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

summary:
We identified two phenotypically and functionally distinct populations in AML-iPSC lines upon hematopoietic differentiation. A cell fraction with a hematopoietic stem cell (HSC) immunophenotype exhibiting adherent growth (iLSCs=samples A) and a fraction of more differentiated cells growing in suspension (iBlasts=samples S).
We used RNA-seq and ATAC-seq analyses to identify molecular differences between the two populations.

overall_design: Comparison of gene expression (RNA-seq) and chromatin accessibility (ATAC-seq) in genetically clonal iLSCs vs iBlasts cells

first: Eirini

last: Papapetrou

first: Michael

last: Kharras

first: Christina

last: Leslie

first: Andriana

last: Kotini

first: Han

last: Yuan

first: Hanzhi

last: Luo


title: Nuclear peripheral positioning of heterochromatin by Amo1NUPL2 suppresses nucleosome turnover to promote epigenetic inheritance

last: Grewal


title: miR-182 and miR-183 act as GDNF mimics in midbrain neurons

city: Göttingen

first: Gaurav

last: Jain

state: Lower Saxony

address: Von-Siebold-Str. 3a, Office no: 2.212

institute: The German Center for Neurodegenerative Diseases (German: Deutsches Zentrum für Neurodegenerative Erkrankungen DZNE)

summary: We found in primary midbrain neurons the expression of miR-182 and miR-183 is increased with the treatment of GDNF. Further we showed that  the transfaction with these two miRNA mimics resulted into the increased neurite length and regeneration in vitro. These mimics also showed neuroprotection of dopamenergic neurons in vitro and in vivo with an effect similar to GDNF. Finally we showed this effect is mediated by the downregulation of Foxo transcription factors.

overall_design: Primary midbrain neurons were cultured for DIV 1 and DIV 5 with or without GDNF supplementation. Cells were collected and total RNA was isolated for smRNA sequencing to compare the effect of GDNF treatment at DIV 1 and DIV 5.

first: Anna-Elisa

last: Roser

first: Lucas

last: Gomes

first: Rashi

last: Halder

first: Fabian

last: Maass

first: Lars

last: Tönges

last: Tatenhorst

first: Mathias

last: Bähr

first: André

last: Fischer

first: Paul

last: Lingor


last: Wesely

summary:
We identified two phenotypically and functionally distinct populations in AML-iPSC lines upon hematopoietic differentiation. A cell fraction with a hematopoietic stem cell (HSC) immunophenotype exhibiting adherent growth (iLSCs =samples A) and a fraction of more differentiated cells growing in suspension (iBlasts = samples S).
We used RNA-seq and ATAC-seq analyses to identify molecular differences between the two populations.

overall_design: Comparison of chromatin accessibility (ATAC-seq) in genetically clonal iLSCs vs iBlasts

last: Papapetrou


summary:
We identified two phenotypically and functionally distinct populations in AML-iPSC lines upon hematopoietic differentiation. A cell fraction with a hematopoietic stem cell (HSC) immunophenotype exhibiting adherent growth (iLSCs =samples A) and a fraction of more differentiated cells growing in suspension (iBlasts =samples S).
We used RNA-seq and ATAC-seq analyses to identify molecular differences between the two populations.

overall_design: Comparison of gene expression (RNA-seq) in genetically clonal iLSCs vs iBlasts

last: Kharras

last: Leslie


title: Xenophagic process controls the Enteroinvasive Escherichia coli infection of the epithelial cells II

city: São Paulo

first: Hadassa Cristhina

middle: Azevedo Soares

last: Santos

state: São Paulo

address: Avenida Professor Lineu Prestes, 580

department: Department of Clinical Chemistry and Toxicology

country: Brazil

institute: University of São Paulo

summary: The invasive bacteria recognition by host cells through autophagy is a key factor for determining bacterial infection. Enteroinvasive Escherichia coli (EIEC) express a protein IcsB, which in Shigella, is known for inactivating the bacterial degradation process. Once EIEC showed less expression of icsB when compared to S. flexneri, we proposed to investigate the autophagy caused by EIEC infection. Our results showed that IcsB protein is an important virulence factor in EIEC because it causes a camouflage of the bacteria in the eukaryotic cell. When there is low or none expression of the protein, the cell recognition of the invasive bacteria is high, decreasing the bacteria dissemination. This found confirms the importance of the gene transcription and the sequence, since the strain E. coli SM124/13, complemented with icsB from Shigella, showed higher dissemination efficiency inside of the host cell. Additionally, our results revealed that eukaryotic cell infected by EIEC or Shigella flexneri showed distinguish responses. In EIEC infection, the autophagy was activated in human cells, but not in a conventional mode. Our hypothesis is that EIEC is recognized by autophagy, being an important cell process for bacterial recognition.

overall_design: Caco-2 transcriptomic profiles with and without bacterial infections were compared in order to identify differentially expressed transcripts at different interaction periods (up to 3 hrs).

first: Hadassa

first: Renato

last: Ramos

middle: G

last: Ferreira

first: Silvia

last: Bando

first: Fernanda

middle: B

last: Bertonha

first: Leandro

first: Carlos

last: Moreira-Filho

first: Cecília

last: Abe

first: Ana

last: Moreno

first: Marina

last: Martinez


title: Xenophagic process controls the Enteroinvasive Escherichia coli infection of the epithelial cells III

first: Lucas

middle: R


title: Hippocampus RNA-seq in CD x Gtf2i*

city: St Louis

first: Joseph

last: Dougherty

state: Missouri

address: 4566 Scott Ave, box 8232

department: Genetics and Psychiatry

institute: Washington University

summary: Williams syndrome is a neurodevelopmental disorder caused by a 1.5-1.8Mbp deletion on chromosome 7q11.23, affecting the copy number of 26-28 genes. Phenotypes of Williams syndrome include cardiovascular problems, craniofacial dysmorphology, deficits in visual spatial cognition, and a characteristic hypersocial personality. There are still no genes in the region that have been consistently linked to the cognitive and behavioral phenotypes, although human studies and mouse models have led to the current hypothesis that the general transcription factor 2 I family of genes, GTF2I and GTF2IRD1, are responsible. Here we test the hypothesis that these two transcription factors are sufficient to reproduce the phenotypes that are caused by deletion of the Williams syndrome critical region (WSCR). We compare a new mouse model with loss of function mutations in both Gtf2i and Gtf2ird1 to an established mouse model lacking the complete WSCR. We show that the complete deletion model has deficits across several behavioral domains including social communication, motor functioning, and conditioned fear that are not explained by loss of function mutations in Gtf2i and Gtf2ird1. Furthermore, transcriptome profiling of the hippocampus shows changes in synaptic genes in the complete deletion model that are not seen in the double mutants. Thus, we have thoroughly defined a set of molecular and behavioral consequences of complete WSCR deletion, and shown that other genes or combinations of genes are necessary to produce these phenotypic effects.

overall_design: 18 samples of total hippocamapal RNA from three genotypes, CD, Gtf2i*, and WT. There are 6 biological replicates per genotype. WT are used as the controls

first: Nathan

last: Kopp


title: Xenophagic process controls the Enteroinvasive Escherichia coli infection of the epithelial cells I


title: Widely distributed neurotensinergic neurons in the brainstem regulate NREM sleep in mice

status: Public on Jan 09 2020

city: Tsukuba-shi

first: Yu

last: Hayashi

address: Tennodai 1-1-1

institute: University of Tsukuba

summary: Microarray identifies enriched expression of Nts in SubLDT, compared to dorsal and ventral area

overall_design: Total RNA was obtained from brainstem tissues of 8-week-old male Chat-Cre: Ai9 mice, and applied for analysis.

first: Shigeyoshi

last: Itohara


title: TGF-β and RREB1 coordinate EMT programs in NMuMG cells

first: Jie

last: Su

address: 1275 York Avenue

institute: Memorial Sloan Kettering Cancer Center

summary: Epithelial-to-mesenchymal transitions (EMT) play prominent roles during development, regeneration and tumor progression. EMTs are triggered by TGF-β, RAS and other signals that cooperatively induce the expression of master EMT transcription factors such as SNAIL. Here, we elucidate how the TGF-β and RAS pathways jointly trigger EMTs and tie them to broader developmental programs. We identify RAS response element binding protein 1 (RREB1) as a critical partner of TGF-β-activated SMAD transcription factors in driving SNAIL expression and EMT program in mammary gland epithelial cells.

overall_design: RNA-seq analyses are used to profile transcriptomic changes of TGF-β treatment in NMuMG cells

first: Joan

last: Massague


title: Next Generation Sequencing Analysis of Wild Type (WT) and SRSF1 knockdown (KD) U87MG and U251 cells Transcriptomes

city: Tianjin

first: Xuexia

last: Zhou

address: 154 Anshan Road

department: Tianjin Neurological Institute

institute: Tianjin Medical University General Hospital

summary: We generated the SRSF1 knockdown U87MG and U251 cells by infecting with shRNA virus. Then, we extracted RNAs and performed next generation sequencing. By comparing sequencing data from WT and KD samples in each cell type, we profiled the alternative splicing events and gene expression regulated by SRSF1 in GBM.

overall_design: WT and KD groups of U87MG and U251 cells mRNA profiling was performed by deep sequencing, using Illumina HiSeq2000.


title: MeDIP-Seq for ALV-J-susceptible and ALV-J-resistant chickens

status: Public on Jan 10 2020

city: Guangzhou

first: Yiming

last: Yan

address: Wushan Road

institute: South China Agricultural University

type: Methylation profiling by high throughput sequencing

summary: We bed ALV-J-susceptible and ALV-J-resistant chickens. In this work, we find the difference DNA methylation states between ALV-J-susceptible and ALV-J-resistant chickens

overall_design: Examination of different DNA methylation states in ALV-J-susceptible and ALV-J-resistant chickens.

first: Yan

last: Yiming


title: TGF-β and RREB1 coordinate EMT programs in development and cancer

summary: Epithelial-to-mesenchymal transitions (EMT) play prominent roles during development, regeneration and tumor progression. EMTs are triggered by TGF-β, RAS and other signals that cooperatively induce the expression of master EMT transcription factors such as SNAIL. Here, we elucidate how the TGF-β and RAS pathways jointly trigger EMTs and tie them to broader developmental programs. We identify RAS response element binding protein 1 (RREB1) as a critical partner of TGF-β-activated SMAD transcription factors in driving SNAIL expression in pancreatic pre-malignant epithelial cells, lung adenocarcinoma cells, and embryonic stem cells. Moreover, SMADs and RREB1 also drive EMT-associated fibrogenic programs in epithelial cells and mesendoderm differentiation in pluripotent embryonic cells. These findings illuminate the orchestration of EMT associated programs in gastrulation, fibrosis, and cancer.

overall_design: RNA-seq, ChIP-seq, and ATAC-seq are used to profile pancreatic organoid, pancreatic adenocarcinoma cells, and embryonic stem cells


title: Genomic Landscape and Therapeutic Targets of Adenosquamous Carcinoma of the Pancreas [CGH Microarray]

status: Public on Jan 08 2020

city: Scottsdale

first: michael

middle: thomas

last: barrett

state: Arizona

address: 13400 east shea boulevard

institute: mayo clinic arizona

summary: We applied DNA content flow cytometry to a series of adenosquamous cancer of the pancreas (ASCP) tumor samples and patient derived xenografts (PDXs). We interrogated purified sorted tumor fractions from each sample with whole genome copy number variant (CNV) and whole exome sequencing (WES) analyses. These identified a variety of somatic genomic lesions targeting chromatin regulators in ASCP genomes that were superimposed on well characterized genomic lesions including mutations in KRAS and TP53, homozygous deletion of CDKN2A, and amplification of c-MYC, that are common in PDACs. Furthermore, a comparison of ATAC-seq profiles of ASCP and pancreatic ductal adenocarcinoma (PDAC) genomes using flow sorted PDX models distinguished genes with accessible chromatin in ASCP genomes including the lysine methyltransferase SMYD2, the pancreatic cancer stem cell driver RORγ, and a FGFR1-ERLIN2 fusion associated with focal CNVs in both genes. Organoids derived from these models were used to screen compounds of interest. Notably a FGFR inhibitor had significant activity against the FGFR1-ERLIN2 fusion positive PDX.

overall_design: We applied DNA content based flow sorting to isolate the nuclei of clonal populations from ASCP tumor biopsies and patient derived xenografts (PDXs). We coupled this strategy with oligonucleotide array CGH (aCGH) and next generation sequencing, thereby obtaining high definition genomic profiles of clonal populations from each tumor. Flow sorted PDXs were used for ATAC-seq analyses of both ASCP and PDAC genomes. Response to FGFR inhibition was assesed with ASCP organoid models.

first: Elizabeth

last: Lenkiewicz

first: Smriti

last: Malasi

first: Martin

last: Fernandez-Zapico

first: Derek

last: Cridebring

first: Tara

middle: L

last: Hogenson

first: Mitesh

last: Borad

first: Kendall

last: Chambers

first: Nirakar

last: Rajbhandari

first: Tannishtha

last: Reya

first: Yuning

last: Xiong

first: Jeong-Heon

last: Lee

first: Zhenqing

last: Ye

first: Huihuang

first: Tamas

last: Ordog

first: Matthew

last: Hernandez

first: Jennifer

last: Leiting

first: Mark

last: Truty

first: Daniel

last: von Hoff

first: Michael

middle: T

last: Barrett


title: Characterization of Holstein and Normande whole milk miRNomes highlights breed specificities

city: Jouy-en-Josas

first: Sandrine

last: Le Guillou

address: Domaine de Vilvert Bat.440

department: Animal Genetics

institute: INRAE

summary: The concept of milk as a healthy food has opened the way for studies on milk components, from nutrients to microRNAs, molecules with broad regulatory properties present in large quantities in milk. Characterization of these components has been performed in several species, such as humans and bovine, depending on the stages of lactation. Here, we have studied the variation in milk microRNA composition according to genetic background. Using high throughput sequencing, we have characterized and compared the milk miRNomes of Holstein and Normande cattle, dairy breeds with distinct milk production features, in order to highlight microRNAs that are essential for regulation of the lactation process. In Holstein and Normande milk, 2,038 and 2,030 microRNAs were identified, respectively, with 1,771 common microRNAs, of which 1,049 were annotated and 722 were predicted. The comparison of the milk miRNomes of two breeds allowed to highlight 182 microRNAs displaying significant differences in the abundance. They are involved in the regulation of lipid metabolism and mammary morphogenesis and development, which affects lactation. Our results provide new insights into the regulation of molecular mechanisms involved in milk production.

overall_design: microRNA profiles of whole milk from 17 primiparous cows (Holstein: four 2-years old and five 3-years old; Normande: three 2-years old and five 3-years old), at 2-months of lactation, generated by deep sequencing, using Illumina HiSeq 4000.

first: Antoine

last: Leduc

first: Johann

last: Laubier

first: Sarah

last: Barbey

first: Marie-Noëlle

last: Rossignol

first: Rachel

last: Lefebvre

first: Sylvain

last: Marthey

first: Denis

last: Laloë

first: Fabienne

last: Le Provost

first: Diane

last: Esquerre


title: The role of micro-ribonucleic acids and extracellular vesicles  in In-Vitro Fertilization

city: Homburg

first: Nicole

last: Ludwig

address: Kirrberger Strasse

department: Human Genetics

institute: Saarland University

summary: BACKGROUND: Molecular signaling in in vitro fertilization procedures seems to play a crucial role for  embryonic development. In a prospective blinded cohort study, we investigated the role of microRNAs  (miRNA) and extracellular vesicles (EV) as potential carriers of miRNAs in embryonic culture media.  METHODS: Embryonic culture media from 56 female partners undergoing infertility treatment.  miRNA microarray and RT-qPCR assays in combination with bioinformatics were used for the screening,  validation and analysis of identified miRNAs. Nanoparticle tracking analysis was applied to measure EV  in culture media.  RESULTS: The overall miRNA repertoire in culture media was astonishingly complex: 621 miRNAs  were present in embryonic culture media. Samples with positive outcome had an overall decreased  miRNA repertoire, with the largest effects for miR-29c-3p. RT-qPCR measurements were largely  consistent with the microarray results. Comparison to human spermatozoa profiles highlighted that a large  part of spermatozoa miRNAs (101 miRNAs) are also present in culture media following embryonic  transfer. As potential carrier molecules that could be of relevance for the decreased miRNA repertoire in  samples with positive outcome we investigated EV in a small proof-of-concept study. While the size  distribution was similar between both cohorts, the total number of EV in pure culture media was zero, in  culture media of patients with positive outcome 3.8 billion per ml and in culture media of samples with  negative outcome 7.35 billion per ml, correlating well with the results for the miRNAs.  CONCLUSIONS: Embryonic culture media of pre-implantation embryos contains a stable population of  highly specific to ubiquitous miRNAs that are correlated to embryogenesis and spermatogenesis  processes. These miRNAs are potentially harbored by EV.

overall_design: We profiled the miRNA repertoire of 56 embryonic culture media after embryos were transferred. In  39 cases the embryo transfer did not lead to a pregnancy while in 17 cases it lead to positive pregnancy.

first: Masood

last: Abu-Halima


title: O-glycan initiation directs distinct biological pathways and controls epithelial differentiation

city: Copenhagen N

first: Hiren

last: Joshi

address: Blegdamsvej 3B

department: ICMM

country: Denmark

institute: Copenhagen University

summary: We used RNA_Seq to quantify cellular transcripts in human spontaneously immortalized HaCaT keratinocytes upon knock out of GALNT1, GALNT2, or GALNT3 - most abundantly expressed enzyme isoforms initiating mucin-type O-linked glycosylation.

overall_design: 3 different knock out clones of each GALNT1, GALNT2, or GALNT3, as well as 2 biological replicates of wild type

first: Emil

middle: H

last: Pallesen

first: Ieva

last: Bagdonaite


title: RNA-Seq Analyses of the apoptosis and necroptosis in MEF

first: Xiaodong

last: Ma

state: Guangdong

address: Rm406,Building 29, South China Normal University

institute: South China Normal University

summary:
Purpose:  we used next generation sequencing to analyze gene expression profiles of MEF treated with PBS (control), TNF-ɑ + Cycloheximide (TC) or TNF-ɑ + Cycloheximide+ z-VAD-fmk (TCZ). The goals of this study are to compare the different gene expression profiles between MEF treated with TC compared to PBS treatment and MEF treated with TCZ compared to PBS treatment.
Methods: In MEF, the combination of TNF-α and cycloheximide (TC) induces apoptosis, whereas the addition of z-VAD-fmk (TCZ) to this regimen promotes necroptosis, using High-seq 2000 Illumina sequencing platform. 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
Results: By comparing the RPKM values between the two groups, a total 492 DEGs (342 upregulated and 150 downregulated) were identified in MEF treated with TC compared to PBS treatment, and a total 424 DEGs (242 upregulated and 182 downregulated) were identified in MEF treated with TCZ compared to PBS treatment. Next, we compared all identified DEGs in MEF between TC and TCZ treatment. We found that 252 DEGs overlapped between TC and TCZ treatment, whereas 240 DEGs were only present in TC treatment and 172 DEGs were only present in TCZ treatment.
Conclusions: we firstly identified 492 DEGs in apoptotic MEF, and as well as 424 DEGs in necroptotic MEF. And we performed the enriched molecular pathway, molecules, transcription factors and signaling networks by IPA analysis. We revealed that apoptosis and necroptosis may share certain common canonical pathways and transcription factors.

overall_design: MEF treated with PBS (control), TNF-ɑ + Cycloheximide (TC) or TNF-ɑ + Cycloheximide+ z-VAD-fmk (TCZ).were generated by deep sequencing every group have 2 sample, using High-seq 2000 Illumina sequencing platform.


title: DNA methylome comparison of low IQ versus high IQ trisomy 21

city: Wuerzburg

first: Tobias

last: Mueller

address: Am Hubland

institute: University of Wuerzburg

summary: Methylomic profiling in trisomy 21 for identification of cognition- and Alzheimer’s disease-related dysregulation.

overall_design: Bisulphite converted DNA from 32 individuals were hybridised to the Illumina Infinium MethylationEPIC BeadChip (11 T21 samples, 8 IQ+ and 3 IQ-, and 21 healthy controls with high IQs)

first: Larissa

last: Haertle

last: Müller

first: Roy

last: Lardenoije

first: Anna

last: Maierhofer

first: Marcus

last: Dittrich

first: Renzo

last: Riemens

first: Samantha

last: Stora

first: Mathilde

last: Roche

first: Markus

last: Leber

first: Steffi

last: Riedel-Heller

first: Michael

last: Wagner

first: Martin

last: Scherer

first: Aimé

last: Ravel

first: Clotilde

last: Mircher

first: Cecile

last: Cieuta-Walti

first: Sophie

last: Durand

first: Daniel

last: van de Hove

first: Per

last: Hoffmann

first: Alfredo

last: Ramirez

first: Thomas

last: Haaf

first: Nady

last: El Hajj

first: André

last: Mégarbané


title: Epithelial to Mesenchymal Plasticity and Differential Response to Therapies in Pancreatic Ductal Adenocarcinoma

city: Boston

first: David

last: Ting

state: MA

address: 149 E 13th street

department: Cancer Center

institute: Massachusetts General Hospital

summary: PDAC epithelial (E) and quasi-mesenchymal (QM) subtypes can be modulated by different therapies demonstrating the plasticity of PDAC cells that contributes to the heterogeneity of PDAC tumors and their intrinsic resistance to a broad spectrum of therapies. Understanding and monitoring the fluidity of PDAC E and QM states are critical to the development of improved clinical trial design to target these different subpopulations

overall_design: PDAC cell lines were grown in 3D culture and treated with chemotherapeutic agents (FOLFIRINOX), Vitamin D (calcitriol) or the appropriate vehicle controls. Tumorspheres were harvested at varying timepoints following treatment for RNA purification, library preparation and next generation sequencing. For some samples including Vit D treatment of PDAC cell lines, experiments were performed in duplicate or triplicate as indicated.

first: Rebecca

last: Porter

first: Neelima

last: Magnus

first: Vishal

last: Thapar

first: Robert

last: Morris

first: Annamaria

last: Szabolcs

first: Azfar

last: Neyak

first: Anupriya

last: Kulkarni

first: Eric

last: Tai

first: Abhijit

last: Chougule

first: Allesandra

last: Hillis

first: Gabriel

last: Golczer

first: Hongshan

last: Guo

first: Teppei

last: Yamada

first: Tomohiro

last: Kurokawa

first: Chittampalli

last: Yashaswini

first: Matteo

last: Ligorio

first: Kevin

last: Vo

first: Linda

last: Nieman

first: Andrew

last: Liss

first: Vikram

last: Deshpande

last: Lawrence

first: Shyamala

last: Maheswaran

first: Carlos

last: Fernandez-Del Castillo

first: Theodore

last: Hong

middle: P

last: Ryan

first: Peter

last: O'Dwyer

first: Jeffrey

last: Drebin

first: Cristina

last: Ferrone

last: Haber


title: Monocyte phenotype, gene expression and plasma biomarkers in HIV-infected longterm ART-suppressed individuals

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Background.  HIV-infected individuals on antiretroviral therapy (HIV/ART) experience higher levels of non-AIDS morbidity than uninfected people, which is believed to be driven by inflammation that persists despite viral suppression.   Elevations in plasma cytokines, coagulation markers and both innate and adaptive immune cell activation during untreated infection are often incompletely reversed by ART and associated with these morbidities.  Monocytes/macrophages play a central role in many of these complications including neurocognitive and cardiovascular disease.    Results.  We investigated monocyte surface markers, gene expression and plasma cytokines in 11 HIV-infected older individuals (median age 53 years) who started therapy with low CD4 counts (median 129 cells/ul), with elevated hsCRP (≥2mg/L) despite long-term ART (median 7.4 years), along with age, gender, race and smoking status-matched controls.  Major monocyte subsets (based on CD14/CD16/CD163) were not different from controls, but surface levels differed for CD163 (p=0.022), PD1 (p=0.015) and a trend for tissue factor (p=0.098).  As a group, HIV/ART subjects had elevated levels of plasma CCL2 (MCP-1; p=0.0001), CXCL9 (MIG; p=0.04) and sIL2R (p=0.015), which were highly correlated, whereas sCD14 and several other markers were not significantly elevated.  However, principal component analysis of soluble markers revealed that about half of HIV/ART subjects clustered with controls, whereas the remainder were distinct, driven by IL-10, CCL11, CXCL10, CXCL11 as well as CCL2, CXCL9 and sIL2R.  Outlier subjects were significantly older than those who clustered with controls.  Gene expression analysis unexpectedly revealed downregulation in HIV/ART monocytes of multiple genes linked to immune functions including inflammation, immune cell development and cell-cell signaling.    Conclusions.  These results reveal a novel pattern of immune dysregulation involving both aberrant inflammation and monocyte dysfunction, which suggests complex mechanisms linking monocytes and HIV/ART comorbidities.

overall_design: Gene expression of purified monocytes from HIV/ART subjects and matched controls

first: Anjana

last: Yadav

first: Ronald

last: Collman


title: Temperature sensitive Mutant Proteome Profiling: a novel tool for the characterization of the global impacts of missense mutants on the proteome

city: Indianapolis

first: Sarah

last: Peck Justice

state: IN

address: 635 Barnhill Dr

department: Biochemistry and Molecular Biology

institute: Indiana University

summary:
RNA-seq experiments measuring global RNA abundance

Temperature sensitive (TS) mutants are a tool that have been foundational for the study of many essential life processes. Despite the long-term use of TS mutants, the mechanisms that lead to temperature sensitivity are not fully understood. Furthermore, a high-throughput workflow to characterize biophysical changes occurring in TS mutants is lacking. We developed Temperature sensitive Mutant Proteome Profiling (TeMPP), a novel application of mass spectrometry based thermal proteome profiling (TPP) as a way to measure the effects of missense mutations on protein stability and protein-protein interactions. This study characterized the global changes in mRNA abundance, protein abundance, and protein thermal stability as a result of missense mutants within two subunits of the yeast ubiquitin-proteasome system. Global protein abundance measurements and RNA sequencing data resulted in a large number of possible candidates that could be causing the phenotypic changes observed in the mutant strains. The additional information gained from TeMPP along with complementary proteomic and transcriptomic experiments allows for multiomic intersection analysis that may reveal interesting regulatory categories to pursue in follow-up mechanistic experiments.

overall_design: Four RNA-Seq biological replicates each for ts mutant (pup2-ts and rpn5-ts) and reference cells (WT)

last: Justice

first: Guihong

last: Qi

first: HR

last: Wijeratne

first: Jose

middle: F

last: Victorino

first: Ed

last: Simpson

first: Aruna

first: Amber

last: Mosley


title: Transcriptional profiling of the adult mouse retina in wild-type and Nrl deficient mice

city: Chicago

first: Ivan

last: Moskowitz

address: 900 E 57th St

department: Pediatrics, Pathology, and Human Genetics

institute: University of Chicago

summary:
We performed mRNA transcriptional profiling of mouse retina in the wild-type and Nrl-null context to determine Nrl-dependent gene expression
We sequenced cDNA libraries made from polyA+ selected RNA from retinas of litter-matched WT and Nrl-/- adult mice at postnatal day 21 (P21) (WT vs Nrl-/-, n=5 and n= 6 resp.)

overall_design: Differential mRNA-seq testing of 21-day old wild type (WT) and Nrl-/- mice  generated from polyA enriched RNA

last: Perez-Cervantes

first: Rangarajan

last: Nadadur

first: Linsin

last: Smith


title: Enhancer transcription identifies cis-regulatory elements for photoreceptor cell types

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

overall_design: Refer to individual Series


title: Transporters and ascorbate–glutathione metabolism for differential cadmium accumulation and tolerance in two contrasting willow genotypes

city: Beijing

first: Yunxing

last: Zhang

address: Dongxiaofu 1

institute: Chinese Academy of Forestry

summary: Comparative transcriptome analysis revealed that higher expressions of several metal transporter genes (ABC transporters, K+ transporters/channels, yellow stripe-like proteins, Zinc regulated transporter/iron-regulated transporter-like proteins, etc.) are involved in root uptake and translocation capacity in HCW

overall_design: Examination of 3 different samples in 2 different willow genotypes.

first: Xiaojiao

last: Han


title: Single Cell RNA-Seq Reveals Changing Landscape of Cell-to-Cell Variation Induced by CTCF Knockdown

city: Shenzhen

first: Wenfei

last: Jin

address: 1088 Xueyuan Rd #faculty research building 1

department: Department of Biology

institute: Southern University of Science and Technology

summary: In this study, we knockdown the expression of CTCF in EL4 cells by shRNA, followed by single cell RNA-seq on both wild type (WT) cells and CTCF-Knockdown (CTCF-KD) cells. Principal component analysis (PCA) of single cell RNA-seq data showed that WT cells and CTCF-KD cells essentially concentrated in two different clusters on the PCA projection, indicating gene expression profiles of CTCF-KD cells and WT cells were systematically different. We further found the cells’ CTCF expression levels were correlated with the cell’s positioning on PCA projection. Interestingly, GO terms including regulation of transcription, DNA binding, Zinc finger and transcription factor binding are significantly enriched in CTCF-KD specific highly variable genes, indicating tissue specific genes such as transcription factors were highly sensitive to CTCF-KD level and showed strongly increased variation. While the housekeeping genes including rRNA processing, DNA repair and tRNA processing are significantly enriched in WT specific highly variable genes, potentially indicating cell-to-cell variation of cell activity in WT cells is higher than that of CTCF-KD cells. We found CTCF-KD cell specific highly variable genes were significantly enriched in CTCF-KD specific down-regulated genes, indicating knockdown of CTCF simultaneously reduced expression levels and increased gene expression noises of its target genes. In summary, analysis of genome-wide cell-to-cell variation in this study showed CTCF-medicated promoter-enhancer interaction not only important for maintaining the expression of its target genes, but also played important roles in reducing the expression noise of its target genes.

overall_design: In this study, we knockdown the expression of CTCF in EL4 cells by shRNA, followed by single cell RNA-seq on both wild type (WT) cells and CTCF-Knockdown (CTCF-KD) cells. To identify the influence of CTCF on genome-wide landscape of cell-to-cell variations.

first: Wei

last: Wang

first: Gang

last: Ren

first: Ni

last: Hong

first: Keji

last: Zhao


title: Gata3 directly regulates cell cycle exit-coupled lens fiber cell differentiation in mouse embryonic lens

city: Bronx

first: Ales

last: Cvekl

state: NY

address: 1300 Morris Park Avenue, Ullman 123

department: The Departments Ophthalmology and Visual Sciences, Genetics

institute: Albert Einstein College of Medicine

summary: Gata3 is a DNA-binding transcription factor involved in cellular differentiation in a variety of tissues. To investigate the role of Gata3 in lens development we conducted lens-specific conditional loss-of-function model of Gata3 and confirmed abnormal regulation of cell cycle exit-coupled lens differentiation and retention of nuclei in the mutated lens fibers. We analyzed transcriptomes between control and mutated lenses by RNA-seq and revealed dysregulation of genes encoding critical components of the lens differentiation cascade, including a subset of crystallin genes, down-regulation of Dnase2b and reduced expression of Cdkn1b/p27 and Cdkn1c/p57.

overall_design: Lens mRNA profiles of E14.5 wild-type (WT) and Gata3 lens-specific knockout (CKO) mice were analyzed by RNA-seq. Each sample represents the pool of 10 lenses from 5 embryos and total number of 3 biological replicates was used for transcriptome sequencing using Illumina HiSeq400 system.

first: Elena

last: Martynova

first: Yilin

first: Qing

last: Xie

first: Paul

last: Overbeek

first: Deyou

last: Zheng


title: Evolutionary transition from degenerate to non-redundant cytokine signaling networks supporting intrathymic T cell development

city: Freiburg im Breisgau

first: Thomas

last: Boehm

address: Stübeweg 51

department: Immunology

institute: MPI-IE Freiburg

summary: In mammals, T cell development in the thymus is critically dependent on the presence of the IL7 cytokine. Here, we describe the identification of the zebrafish ortholog of mammalian IL7, based on chromosomal localization, expression patterns, and deduced protein sequence. To examine the biological role of il7 in teleosts, we generated an il7 allele lacking most of its coding exons using CRISPR/Cas9-based mutagenesis. il7-deficient animals are viable, and exhibit no obvious signs of immune disorder. With respect to intrathymic T cell development, il7-deficiency is associated with only mild a reduction of thymocytes, contrasting with the much stronger reduction of T cell development il7r-deficient fish. Genetic interaction studies between il7 and crlf2(tslpr) suggest the contribution of an additional, as yet unidentified cytokine(s) to intrathymic T cell development. Such activities were also ascertained for other cytokines, such as il2 and il15, collectively indicating that, in contrast to the situation in mammals, T cell development in the thymus of teleosts is driven by a degenerate multi-component network of gc cytokines. This network configuration thus explains why deficiencies of single components have little detrimental effect. By contrast, the dependence on a single cytokine in the mammalian thymus has catastrophic consequences in case of congenital deficiencies in genes affecting the IL7 signaling pathway. We speculate that the transition from a degenerate to a non-redundant cytokine network supporting intrathymic T cell development emerged as the consequence of repurposing evolutionary ancient constitutive cytokine pathways for regulatory functions in the mammalian peripheral immune system.

overall_design: The experiments aimed at identifying the role of the il7 cytokine in lymphocyte development of zebrafish. The transcriptomes of whole kidney marrow in wild-type and il7 mutant fish were compared for differences in expression levels

first: D

last: Lawir

first: K

last: Sikora

first: T


title: Multi-level transcriptome sequencing identifies COL1A1 as a candidate marker in human heart failure progression

first: Jiangping

last: Song

address: 167A Beilishi Road, Xi Cheng District

department: Department of Cardiac Surgery

institute: Chinese Academy of Medical Sciences and Peking Union Medical College

summary:
Background: Heart failure (HF) has been recognized as global pandemic with a high rate of associated hospitalization, morbidity and mortality. Although numerous advances have been made, its representative molecular signatures remain largely unknown, especially the role of genes in HF progression. The aim of the present prospective follow-up study was to reveal potential biomarkers associated with the progression of heart failure.

Methods: We collected left ventricular heart tissue from 21 HF patients and 9 healthy donors as study cohort and generated multi-level transcriptomic data. By using Masson staining to calculate the fibrosis percentage for each sample, we applied lasso regression model to identify the genes associated with fibrosis as well as progression. The genes were further validated by immunohistochemistry (IHC) staining in the same cohort and qRT-PCR using another independent cohort (20 HF and 9 healthy donors). Enzyme linked immunosorbent assay (ELISA) was used to measure the plasma level in validation cohort (87 HF patients) for predicting HF progression.

Results: Based on the multi-level transcriptomic data, we examined differentially expressed genes [mRNAs, microRNAs, and long non-coding RNAs (lncRNAs)] in study cohort. The follow-up functional annotations and regulatory network reveal their potential roles in regulating extracellular matrix. We further identified several genes that were associated with fibrosis. By using the survival time before transplantation, COL1A1 was identified as a potential biomarker for HF progression and its up-regulation was confirmed by both IHC and qRT-PCR. Furthermore, COL1A1 content >281.7 ng/ml in plasma was found to be associated with poor survival within one year of heart transplantation from heart failure [Hazard Ratio (HR): 27.52, 95% Confidence Interval (CI): 7.474 to 101.3, Log-rank p-value<1.0×10-4].

Conclusions: Our results suggested that COL1A1 is a plasma biomarker of HF and associated with HF progression, especially to predict the 1-year survival from HF onset to transplantation.

overall_design: Multi-level transcriptomic data of 21 HF patients and 9 healthy donors were generated by deep sequencing.

first: Xiumeng

last: Hua


title: Overexpression of a Medicago truncutula homeodomain finger protein, MtPHD6, enhances drought tolerance in Arabidopsis

city: Wuhan

first: Zhulong

last: Chan

state: Hubei Province

address: No. 1, Shizishan St, Nanhu

department: College of Horticulture and Forestry Sciences

institute: Huazhong Agricultural University

summary:
Purpose: We aimed to dissect function of Medicago truncutula homeodomain finger protein, MtPHD6 in Arabidopsis
Methods: A total amount of 3 μg RNA was used for generation of sequencing libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. After cluster generation, the library preparations were sequenced on an Illumina Hiseq platform and 125 bp/150 bp paired-end reads were generated. Clean reads were obtained by removing low quality reads, reads containing adapter and ploy-N from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. Index of the Arabidopsis genome was built using Bowtie v2.2.3 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.12. HTSeq v0.6.1 was used to count the reads numbers mapped to each gene. And then FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length of the gene and reads count mapped to this gene. Differential expression analysis of drought stress versus control condition was performed using the DESeq R package (1.18.0).
Results:In total, four samples with three biological replicates per genotype/treatment combination were used for RNA sequencing analysis. At least 2 G clean bases were generated for each sample. Comparative analysis revealed different networks which were modulated by drought stress and MtPHD6 transgene in Arabidopsis seedlings

overall_design: In this researchstudy, M. truncatula Jemalong A17 and Arabidopsis A. thaliana Columbia were wild-type (WT) Col-0 was used as control. After surface-sterilization in 50% (v/v) bleach with 0.01% (v/v) TritonX-100, Arabidopsis seeds were stratified in deionized water at 4 °C for 3 d in darkness. Then the seeds were sown on the full-strength Murashige and Skoog (MS) medium containing 1% (w/v) sucrose and 0.8% (w/v) agar (pH 5.7) in a growth room. The growth room was maintained at 21～23 °C with an irradiance of 100～120 μmol photons m−2 s−1, 60% relative humidity, and a 16 h light/8 h dark cycle. After growth for 7 d on the MS medium, the seedlings, except those used in germination tests, were transferred into soil-filled plastic containers and irrigated with nutrient solution twice each week.

first: Wenli

last: Quan


title: Non-coding Transcriptional profiling of the adult mouse retina in wild-type and Nrl deficient mice

first: Ivan

last: Moskowitz

state: IL

summary: We performed non-coding transcriptional profiling to identify Nrl-dependent ncRNAs by deep sequencing non-polyadenylated RNA from the same control and Nrl-/- retinal samples.  non-coding RNA profiling is a robust method for the identification of cell-type specific functional enhancer elements in the mouse retina

overall_design: Examination of non-coding differential expression between 5 wild-type and 6 knockout samples

first: Carlos

last: Perez-Cervantes

first: Linsin

last: Smith

first: Rangarajan

last: Nadadur


title: Rosellinia necatrix RNA-seq infecting avocado roots

city: Malaga

first: Maria

middle: Clara

last: Pliego

state: Malaga

address: Cortijo de la Cruz s/n

institute: IFAPA Centro de Malaga

summary: White root rot disease caused by Rosellinia necatrix is one of the most important pathogens affecting avocado productivity in temperate, tropical and subtropical climates. Control of this disease is complex and nowadays, lies in the use of physical and chemical methods, although none have proven to be fully effective. Detailed understanding of the molecular mechanisms underlying white root rot disease has the potential of aiding future developments in disease resistance and management. In this regard, this study used RNAseq technology to compare the transcriptomic profiles of R. necatrix during infection of susceptible avocado `Dusa´ roots with that obtained from the fungus cultured in rich medium.  The transcriptomes from three biological replicates of R. necatrix colonizing avocado roots (RC) and R. necatrix growing on potato dextrose agar media (PDA) were obtained using Illumina sequencing. A total of 12,104 transcripts were obtained, among which 1937 were differentially expressed genes (DEG), 137 exclusively expressed in RC and 160 and PDA. Interestingly genes involved in the production of fungal toxins, detoxification of toxic compounds, hormone biosynthesis, gene silencing and plant cell wall degradation were overexpressed during the infection process. In addition, 23 out of the 137 contigs, only expressed during R. necatrix growth on avocado roots, were predicted as candidate effector proteins (CEP) by the CSIRO tool with a probability above 60%. The PHI (Pathogen Host Interaction) database revealed that 11 R. necatrix CEP were previously annotated as effectors genes proven experimentally via pathogen-host interaction.

overall_design:
The analysis of the full-length transcriptome of R. necatrix during the infection process suggested that the success of this fungus to infect diverse crops might be attributed to the production of an extensive array of compounds which singly or in combination likely interfere with structural and functional features shared among different plant families. The transcriptome analysis of R. necatrix during the infection process will provide useful information and facilitate further research to a more in -depth understanding of the biology and virulence of this pathogen. This in turn, will make possible to evolve novel strategies for white root rot management in avocado.
The transcriptomes from three biological replicates of R. necatrix colonizing avocado roots (RC) and R. necatrix growing on potato dextrose agar media (PDA) were obtained using Illumina sequencing.

first: A

last: Zumaquero

first: S

last: Kanematsu

first: H

last: Nakayashiki

last: Matas

first: E

last: Martínez-Ferri

last: Barceló

first: F

last: Pliego-Alfaro

first: C

last: López-Herrera

middle: M

last: Cazorla


title: The Genetic Basis of Aneuploidy Tolerance in Wild Yeast

city: Madison

first: Audrey

last: Gasch

state: WI

address: 425G Henry mall

department: Genetics

institute: University of Wisconsin

summary: Aneuploidy, in which cells carry an abnormal chromosome count, is detrimental during development yet common in human cancers;  why cells differ in tolerance remains unclear.  We mapped the genetic basis of aneuploidy tolerance in wild Saccharomyces cerevisiae versus the sensitive lab strain to Ssd1, an RNA-binding protein involved in translation whose loss recapitulates aneuploidy signatures in laboratory yeast.  We find Ssd1 localizes to mitochondria, influences localization of nuclear-encoded mitochondrial mRNAs and/or abundance of the encoded proteins, influences mitochondrial function, and minimizes protein aggregates upon chromosome amplification.  Recapitulating ssd1D defects with combinatorial drug treatment selectively targets wild-type aneuploids in multiple strains, suggesting therapeutic approaches.  Our work adds to elegant studies done in the sensitized laboratory strain to present a mechanistic understanding of aneuploidy tolerance in eukaryotes.

overall_design: RNA-seq and transcriptome analysis of S. cerevisiae aneuploids YPS1009, NCYC110 having SSD1 deleted. Biological triplicate was minimally performed for RNA-seq. RIP-seq analysis of YPS1009 having SSD1 tagged with GFP, in biological duplicate.

first: James

last: Hose


title: Integrated analysis of microRNA and mRNA expression profiles of rice seedlings in response to zinc deficiency and recovery (mRNA-seq)

city: Hangzhou

first: Houqing

last: Zeng

address: NO.2318, Yuhangtang Rd, Yuhang District

institute: Hangzhou Normal University

summary: Using Illumina’s high-throughput small RNA sequencing and RNA sequencing, miRNAs and mRNAs differentially expressed under Zn deficiency and Zn resupply conditions were identified in shoots and roots of rice seedlings. A total of 68 miRNAs were identified to be differentially expressed under Zn deficiency and/or Zn resupply, and 38 of them were novel miRNAs. The Zn-responsive miRNAs were predicted to target a total of 799 genes. The transcriptome sequencing identified a total of 360 differentially expressed genes (DEGs) under Zn deficiency in shoots and roots, and 97 of them were recovered after Zn resupply treatment. Twelve DEGs were found to be potential targets genes of several Zn-responsive miRNAs like miR171g-5p, miR397b-5p, miR398a-5p, and miR528-5p.

overall_design: Roots and shoots of rice seedlings were collected after Zn-deficient treatment for two weeks. For Zn-resupply treatment, Zn-deficient seedlings were transferred to nomal nutrient solution containing 1.5 µM ZnSO4 for three days. After Zn-resupply treatment, roots and shoots were collected for analyses at the same time point as collecting the Zn-deficient samples (four hours after illumination).


title: Integrated analysis of microRNA and mRNA expression profiles of rice seedlings in response to zinc deficiency and recovery

sample_organism:
Oryza sativa
Oryza sativa Japonica Group


title: Gene expression data of ovarian clear cell carcinoma from Singapore

city: Singapore

first: Tuan Zea

last: Tan

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

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

summary: Ovarian clear cell carcinoma (OCCC) is an epithelial ovarian cancer (EOC) histology having distinct pathology, biology, and molecular footprints. OCCC is chemo-resistant and has the worst stage-adjusted prognosis amongst EOC. Yet, treatment for OCCC patients is no different than other EOC. As OCCC incidence rate has significantly increase in recent decades, it is critical to find OCCC-tailored therapeutic. However, majority of EOC gene expression molecular subtypes (GEMS) studies for personalized medicine focused on the high grade serous histology, and studies in OCCC GEMS were of small sample size. Using more than 200 OCCC gene expression profiles, we identified two OCCC subtypes: EpiCC—epithelial-like, early stage, good prognosis, relative higher rate of gene mutations in SWI/SNF complex; and MesCC—mesenchymal-like, late stage, and poor prognosis. The differential prognosis between EpiCC and MesCC could be observed as early as stage IC. Genetic, copy number and transcriptome profiling showed that both EpiCC and MesCC carried OCCC-associated aberrations. The EpiCC and MesCC are reproducible in validation cohorts and OCCC cell lines. Cell lines assays showed that MesCC is more proliferative and more anoikis resistant than EpiCC. Both EpiCC and MesCC are resistant to cisplatin. Applying the OCCC subtypes to TCGA 534 renal clear cell carcinoma indicated interoperability of the subtyping scheme, and revealed preferential response of EpiCC to sorafenib, and MesCC to bevacizumab. The EpiCC and MesCC classification shows promise in prognostication utility especially for stage IC OCCC patients, and warrants further investigation for subtype-tailored treatment regimen.

overall_design: Frozen archival epithelial ovarian cancer tumors samples of clear cell histology from Department of Obstetrics & Gynecology, National University of Singapore dated from 2006 to 2014 were collected and subjected to microarray analysis.

first: Ruby

middle: Y

last: Huang

first: Jieru

last: Ye

first: Tuan

middle: Z


title: The transcriptome analysis of regulatory networks  in RA-FLSs

city: Guangzhou

first: Bi

last: Xuan

address: No. 600 Tianhe Road, Tianhe District

department: Department of Internal Medicine,

institute: The Third Affiliated Hospital of Sun Yat-sen University

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

summary: Rheumatoid arthritis (RA) is a common chronic inflammatory joint disease characterized by persistent synovial hyperplasia and progressive destruction of joint cartilage and bone.Fibroblast-like synoviocytes (FLSs), a prominent component of hyperplastic synovial pannus tissue, are the primary effector cells in RA synovial hyperplasia and invasion.  However, the underlying molecular mechanisms remain unclear. Here, we apply transcriptome to assay the regulatory networks which contribute to the proliferation, migration and invasion of RA-FLSs .

overall_design: We investigated the differential expression profiles of mRNA and lncRNA in FLSs between two groups: the RA group (fibroblast-like synoviocytes of rheumatoid arthritis patients ), the healthy control groups (fibroblast-like synoviocytes of patients who underwent arthroscopic surgery for knee meniscus injuries or cruciate ligament rupture and had no medical history of acute or chronic joint abnormalities or systemic disease). The data of each group are collected from independent experiments in triplicate. Transcriptomic analysis was carried out using a microarray (Arraystar Human lncRNA Gene Expression Microarrays V4.0; Agilent Technology, Santa Clara, USA), which includes about 40,173 LncRNAs and 20,730 coding transcripts.

first: Xuan

last: Bi

first: YunFeng

last: Pan


city: South San Francisco

first: Steffen

last: Durinck

address: 1 DNA Way

institute: Genentech

summary: validate and study CRISPR/Cas9 knock down line by RNA-seq

overall_design: 4 cell line samples from CRISPR/Cas9 study for bulk RNA-seq

first: Wenlin

last: Yuan

first: Zora

last: Modrusan

first: Leonard

last: Goldstein


title: Study differentially expressed genes comparing metastatic sarcomatoid carcinomas vs adenocarcinomas

summary: compare expression of two groups of tumors

overall_design: 10 tumors samples: 5 metastatic sarcomatoid carcinomas, and 5 adenocarcinomas


title: Positive roles for Osa-miR7695 in regulating defense responses against the rice blast fungus

city: Bellaterra

first: Blanca

last: San Segundo

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Plant Responses to Stress

institute: Center for Research in Agricultural Genomics (CRAG)

summary: MicroRNAs (miRNAs) are small non-coding RNAs that function as post-transcriptional regulators of gene expression in eukaryotes. In rice, miR7695 targets an alternatively spliced transcript of natural resistance-associated macrophage protein 6 (OsNramp6) encoding an iron transporter whose expression is regulated by infection with the rice blast fungus Magnaporthe oryzae. Rice plants grown under high iron supply showed blast resistance, which supports that iron is a factor in controlling blast resistance by still unknown mechanisms. Here, iron accumulated near M. oryzae appressoria, the sites of pathogen entry, and in cells surrounding infected regions of the rice leaf. Activation-tagged MIR7695 rice plants (MIR7695-Ac) exhibited enhanced resistance to M. oryzae infection. RNA-seq analysis revealed that blast resistance in MIR7695-Ac plants was associated with strong induction of defense-related genes, including pathogenesis-related and diterpenoid biosynthetic genes. Levels of phytoalexins during pathogen infection were higher in MIR7695-Ac than wild-type plants. Early phytoalexin biosynthetic genes, OsCPS2 and OsCSP4, were highly upregulated in rice plants grown under high iron supply. Our data indicate that miR7695 positively regulates rice immunity while establishing links between defense and iron signaling in rice. MiR7695-mediated regulation of OsNramp6 has great potential for the development of strategies to control rice blast disease.

overall_design: 8 samples in total: 2 genotypes (WT-Az, MIR7695-Ac) with 2 treatments (Control, Infected), 2 biological replicates each. Samples are: WT-Az (Control); MIR7695-Ac (Control); WT-Az (Infected); MIR7695-Ac (Infected)

first: Ferrán

last: Sánchez-Sanuy

first: Cristina

last: Peris-Peris

first: Shiho

last: Tomiyama

first: Kazunori

last: Okada

first: Yue-Ie

last: Hsing

first: Sonia

last: Campo


title: Study gene expression in mouse mammary tumors single cell RNA-seq, study CRISPR/Cas9 knock down line by RNA-seq

overall_design: 5 tumor samples for single-cell RNA-seq