title: High-temporal-resolution transcriptome analysis of the anti-IgM-stimulated mouse B cells

city: Suita, Osaka

first: Mariko

last: Okada

address: 3-2 Yamadaoka

department: Institute for Protein Research

institute: Osaka University

summary: B cell receptor (BCR) is essential in activating B cells and mediating the immune responses. Analyzing the BCR-triggered gene expression would help delineate the regulatory function of B cells. The mouse B cells were treated with anti-IgM mAb to mimic the BCR stimulation, and the genome-wide transcriptional responses were analyzed by using high-throughput sequencing at high-temporal resolution (24 time points over 6 hours).

overall_design: The mouse splenic B cells were isolated and purified by depleting CD43+ cells. The purified B cells were stimulated with 10 µg/ml of anti-IgM. The gene expression profiles under the anti-IgM stimulation were measured every 15 minutes in the time span from 0 time to 6 hours by RNA-seq analysis using Illumina HiSeq platform. Control was set as the non-stimulated (0 time) cells. Biological replicate samples were analyzed.

first: Hisaaki

last: Shinohara


title: Chromatin remodeling mediated by ARID1A is indispensable for normal hematopoiesis in mice (RNA-Seq)

status: Public on Apr 09 2019

city: Singapore

first: Pushkar

last: Dakle

address: 14 Medical Drive, #12-01,

country: Singapore

institute: Cancer Science Institute of Singapore

type: Expression profiling by high throughput sequencing

summary: ARID1A is a component of the mammalian SWI/SNF complex involved in chromatin remodeling. A functional SWI/SNF complex is required for diverse physiological processes including hematopoiesis, however, the precise role played by ARID1A in hematopoietic development is unclear. Here we utilize hematopoietic cell-specific deletion of Arid1a in mice to uncover its role during adult hematopoiesis. We demonstrate that ARID1A is essential for maintaining the frequency and function of hematopoietic stem cells and its loss impaired the differentiation of both myeloid and lymphoid lineages. ARID1A deficiency led to a global reduction in open chromatin and ensuing transcriptional changes affected key genes involved in hematopoietic development. We also observed that silencing of ARID1A affected ATRA-induced differentiation of NB4 cells, suggesting its role in granulocytic differentiation of human leukemic cells. Overall, our study provides a comprehensive elucidation of its function in hematopoiesis and establishes ARID1A as a major regulator of chromatin dynamics in hematopoietic cells.

overall_design: Differential gene expression in CMP, GMP, MEP and LT-HSC populations between WT and ARID1A knockout mice

first: Lin

last: Han

first: Vikas

last: Madan

first: Anand

last: Mayakonda

first: Weoi

middle: W

last: Teoh

first: Pavithra

last: Shyamsunder

first: Hazimah

middle: M

last: Nordin

first: Cao

last: Zeya

first: Janani

last: Sundaresan

first: Ienglam

last: Lei

first: Zhong

last: Wang

first: H

middle: P

last: Koeffler


title: Estimating Genome-wide Off-Target Effects for Pyrrole-Imidazole Polyamide Binding by a Pathway-Based Expression Profiling Approach (CHP-134 cells)

city: Chiba

first: Jason

last: Lin

state: Chiba

address: 666-2 Nitona-cho, Chuo-ku

country: Japan

institute: Chiba Cancer Center Research Institute

summary: Side and off-target effects remain a difficult issue in the search of pharmaceutical leads, especially with DNA-binding molecules or genome editing methods where the issue becomes particularly thorny. A particular case is the investigations into the off-target effects of N-methylpyrrole-N-methylimidazole polyamides, a naturally inspired class of DNA binders that discriminately access the minor groove with strong affinity and sequence specificity but the relatively short motif of < 20 bases often imply possible non-unique genomic binding. Multiple binding sites may translate to binding at non-intended loci, potentially leading to off-target effects, issues that very few approaches are able to address to-date.  We here report an analytical method of inferring off-target binding from expression profiling based on the relative impact to various biochemical pathways, as well as an accompanying side effect prediction engine to allow candidate polyamides to be systematically screened. This method marks the first attempt in PI polyamide research to identify elements in various biochemical pathways sensitive to the treatment of a candidate polyamide to infer possible off-target effects. Expression changes were then considered for their possible effect on outward phenotypic changes, manifested as side effects, should the same PI polyamide candidate be administered clinically. We also performed a series of animal experiments to validate some of these effects, and found some corroboration in certain side effect manifestations, such as changes in the level of aspartate transaminase in ICR and nude mice after injection of some of the candidate polyamides in this study.

overall_design: O(4) to O(5) cells per condition were plated in a 6-well microtiter plate for overnight attachment prior to treatment of candidate polyamides or 0.05% DMSO. After RNA extraction with RNeasy Plus Mini Kit (Qiagen), labelled with RNA Spike-In Kit and analyzed on SurePrint G3 Human GE 8x60K V2 microarrays.

first: Hiroyuki

last: Yoda

first: Takatori

last: Atsushi


title: Chromatin remodeling mediated by ARID1A is indispensable for normal hematopoiesis in mice (human RNA-Seq)

overall_design: RNA-sequencing of control (LacZ sg) and ARID1A-deficient (sg1 and sg5) NB4 cells. Cells were treated with doxycycline for 7 days.


title: Ascarids exposed: gene expression analysis of anthelmintic naïve Parascaris spp. following in vitro drug exposure

status: Public on Apr 10 2019

city: Lexington

first: Martin

middle: K

last: Nielsen

state: KY

address: 1400 Nicholasville Road

country: USA

institute: University of Kentucky

summary: Ascarid parasites infect a variety of hosts, and control measures rely heavily on anthelmintics raising concerns for anthelmintic resistance. Parascaris spp., the equine ascarid, is the only ascarid with documented substantial drug resistance. Elucidating drug responses of susceptible parasites may lead to further understanding of anthelmintic resistance mechanisms, identifying alternative drug targets, and parameters for slowing the development of resistance among other ascarid species. The purpose of this study was to examine the response of anthelmintic naïve Parascaris spp. to in vitro drug exposure using transcriptomic analyses and quantitative PCR. Adult Parascaris spp. worms were obtained at necropsy from foals born into a herd kept without anthelmintic treatment. Adult worms were maintained in Roswell-Park Memorial medium 1640. The drugs employed were oxibendazole (OBZ) and ivermectin (IVM), and 10-fold serial dilutions were prepared. Optimum drug concentration and exposure length were determined using a worm viability assessment method. Subsequently, RNA-seq analysis identified genes with significantly different expression between drug treated and control groups. Finally, a selection of the significant genes was further investigated using qPCR in a repeat drug exposure trial. Following initial viability assessments, OBZ (10 μg/mL) for 24 hours and IVM (1 μg/mL) for three hours were the conditions employed. RNA-seq analysis revealed a total of 88 transcripts with significantly (α=0.01) different expression between all drug treated and control worms. The top five genes selected for further analysis were snap25, cytochrome p450, kelch10, sup9, and ferm. Gene functionalities are related to muscle contraction, detoxification and exocytotic events, and regulatory processes. qPCR did not identify any significant differences between groups, but this may be due to the lack of method sensitivity. The results of RNA-seq analysis and gene function warrant further investigation and their role in ascarid xenobiotic responses.

overall_design: Total Number of Samples: 10. In vivo control female, In vivo control male, Ivermectin treated female, Ivermectin control female, Ivermectin treated male, Ivermectin control male, Oxibendazole treated female, Oxibendazole control female, Oxibendazole treated male, Oxibendazole control male.

first: Jessica

middle: A

last: Scare

first: Pouya

last: Dini

first: Jamie

last: Norris

first: Ashley

middle: E

last: Steuer

first: Kirsten

last: Scoggin

first: Holli

middle: S

last: Gravatte

first: Daniel

last: Howe

first: Paul

last: Slusarewicz


title: A mouse model featuring tissue specific deletion of p53 and Brca1 gives rise to mammary tumors with genomic and transcriptomic similarities to human basal-like breast cancer [expression]

city: Chapel Hill

first: Charles

middle: M.

last: Perou

state: NC

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

department: Professor of Genetics, and Pathology & Laboratory Medicine; Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: In human basal-like breast cancer, mutations and deletions in TP53 and BRCA1 are frequent oncogenic events. Thus, we interbred mice expressing the CRE-recombinase with mice harboring loxP sites at TP53 and BRCA1 (K14-Cre; p53F/F Brca1F/F) to test the hypothesis that tissue specific deletion of TP53 and BRCA1 would give rise to tumors reflective of human basal-like breast cancer. In support of our hypothesis, these transgenic mice developed tumors that express basal-like cytokeratins and intrinsic gene expression features similar to human basal-like tumors. Array comparative genomic hybridization revealed a striking conservation of copy number alterations between the K14-Cre; p53F/F Brca1F/F mouse model and human basal-like breast cancer. Conserved events included MYC amplification, KRAS amplification, and RB1 loss. Microarray analysis demonstrated that these DNA copy number events also led to corresponding changes in signatures of pathway activation including high proliferation due to RB1 loss. K14-Cre; p53F/F Brca1F/F also matched human basal-like breast cancer for a proposentity to have immune-cell infiltrates. Given the long latency of K14-Cre; p53F/F Brca1F/F tumors (~250 days), we created tumor syngeneic transplant lines, as well as in vitro cell lines, which were tested for sensitivity to carboplatin and paclitaxel. These therapies invoked acute regression, extended overall survival, and resulted in gene expression signatures of an anti-tumor immune response. These findings demonstrate that this model is a valuable preclinical resource for the study of human basal-like breast cancer.

overall_design: Agilent gene expression microarrays were performed on K14-Cre; p53 f/f Brca1 f/f primary tumors, tumor transplant lines, and tumor cell lines. A subset of tumors were profiled during a time-course study of chemotherapy treatment as annotated.

last: Hollern

first: Cristina

last: Contreras

first: Stephanie

last: Dance-Barnes

first: Grace

middle: O

last: Silva

first: Adam

middle: D

last: Pfefferle

first: Jessie

last: Xiong

first: Kelly

last: Clark

first: David

middle: B

last: Darr

first: Jerry

last: Usary

first: Kevin

middle: R

last: Mott


title: Normothermic machine perfusion (NMP) inhibits proinflammatory responses in the liver and promotes regeneration

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

summary: Background and Aims: Liver transplantation is a successful treatment for patients with liver failure. However, organ shortage results in over 11% of patients loosing their chance of a transplant due to worsening of their liver disease. Ischemia/reperfusion injury (IRI) is the major cause leading to graft loss after liver transplantation. Therefore, novel methods of organ-preservation have been developed in recent years to minimize IRI. One such device is the OrganOx metra, a normothermic machine perfusion (NMP) device providing oxygen and nutrition to allow aerobic metabolism and minimizing IRI. OrganOx metra has presented with several advantages compared to conventional cold storage (CS). We aimed to confirm the impact of NMP on reducing IRI and to define the underling mechanisms.  Methods: We compared 12 NMP with 27 CS-preserved livers by performing gene microarray, immunoprofiling of hepatic lymphocytes and immunochemistry staining of liver tissues for assessing necrosis, platelet deposition and neutrophil infiltration, and the status of steatosis after NMP or CS pre- and post-reperfusion.  Results: Recipients receiving NMP grafts showed significantly lower peak AST levels than those receiving CS grafts. NMP altered gene-expression profiles of liver tissue from pro-inflammation to pro-healing and regeneration. NMP also reduced the number of IFN- and IL-17 producing T cells and enlarged CD4posCD25highCD127negFOXP3pos Treg pool. NMP liver tissues showed less necrosis and apoptosis in the parenchyma and fewer neutrophils and platelet infiltration compared to CS liver tissues. Conclusion: Reduced IRI in NMP recipients was the consequence of the combination of inhibiting inflammation and promoting graft regeneration.

overall_design: Gene expression of 15 NMP with 11 preserved livers (CONTROL) under pre- and post-reperfusion.

first: W

last: Jassem

first: E

last: Xystrakis

first: Y

middle: G

last: Ghnewa

first: J

middle: J

first: A

last: Sanchez

last: Ma


title: Gene expression profile of 293T cells transfected with DOCK10

status: Public on Apr 11 2019

city: Murcia

first: Antonio

last: Parrado

address: Ctra. Madrid-Cartagena, s/n

institute: Hospital Clinico Universitario Virgen de la Arrixaca

summary: The goal of this study was to identify changes in the gene expression profile (GEP) of 293T cells in response to transfection with DOCK10 during 24 hours.

overall_design: Human embryonic kidney 293T cells, highly transfectable fibroblastoid cells growing adherently as monolayers, were cultured in Dulbecco’s MEM supplemented with 10 % FCS, 50 U/ml penicillin, 50 U/ml streptomycin, 2,5 µg/ml amphotericin B, and 2 mM L-glutamine. Cells were transfected at subconfluency with pSG5-HA-DOCK10.1 plasmid or empty pSG5 plasmid using lipofectamine, and cultured for 24 hr. Following detachment of cells with 0.05%-EDTA 0.02% in PBS, total RNA was isolated using the miRNeasy Mini Kit (Qiagen) and labeled with cyanine 5-CTP. Total RNA isolated from untransfected 293T cells was labelled with cyanine 3-CTP and used as reference sample. Both 293T samples (pSG5 and DOCK10), were labelled with cy5 and used as test samples. The reference sample and the test samples were hybridized together onto Agilent Whole Human Genome Microarrays (4×44K) targeting 19,596 Entrez Gene RNAs (technology 014850), scanned in an Agilent G2565CA DNA Microarray Scanner using the Agilent Scan Control software. Images were analyzed with the Agilent Feature Extraction software, which computes log ratios (test vs reference) following normalization correction by linear and Lowess methods.


title: Next Generation Sequencing Facilitates Quantitative Analysis of WT and dek15 mutant Transcriptomes

city: Beijing

first: Yonghui

last: He

address: No.2 Yuanmingyuan West Rd, Haidian District, Beijing 100193, China

country: China

institute: China Agricultural University

summary: Analysis of gene expression level. The hypothesis tested in the present study was that dek15 mutant affects nutrient metabolism and cell cycle.

overall_design: mRNA profiles of 15 DAP wild type (WT) and dek15 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 (Zea mays).

first: Rentao

last: Song


title: Exhaustive screening of outer hair cell-specific genes

city: Tokyo

first: Kunie

last: Matsuoka

address: 2-1-6 Kami-kitazawa

institute: Tokyo Metropolitan Institute of Medical Science

summary: Mechanosensory outer hair cells (OHC) play an essential role in the amplification of sound-induced vibrations in the cochlea because of their ability to contract or elongate following changes in the intracellular potential. To study the critical roles of OHC, we generated a novel mouse model, OHC-TRECK, for hearing impairment by introducing the human diphtheria toxin (DT) receptor gene under the control of the OHC-specific promoter of the mouse prestin gene. DT administration to OHC-TRECK mice resulted in severe hearing impairment with a decrease in the amplitude of distortion product otoacoustic emissions and elevated auditory brainstem responses. We performed a differential expression analysis between DT-administered OHC-TRECK and wild-type mice using high-throughput microarray analysis to screen for novel, specifically expressed and functional genes involved in the development and maintenance of OHC.

overall_design: Gene expression in the cochlea (n = 8; 4 females and 4 males) from DT- and DT+ wild-type and OHC-TRECK mice was measured.

first: Yasumasa

last: Nishito


title: RNA-sequencing across three matched tissues highlights gene expression signatures in COPD

city: Boston

first: Jarrett

last: Morrow

state: MA

address: 181 Longwood Ave.

department: Channing Division of Network Medicine

institute: Brigham and Women's Hospital

summary: Multiple gene expression studies have been performed separately in peripheral blood, lung, and airway tissues to study COPD. We performed RNA-sequencing gene expression profiling of large-airway epithelium, alveolar macrophage and peripheral blood samples from the same set of COPD cases and controls from the COPDGene study who underwent bronchoscopy at a single center. Using statistical and gene set enrichment approaches, we sought to improve the understanding of COPD by studying gene sets and pathways across these tissues, beyond the individual genomic determinants.

overall_design:
We performed differential expression analysis using RNA-seq data obtained from 63 samples from 21 COPD cases and controls (includes four non-smokers)
NOTE: Submitter declares that the raw data will be submitted to dbGaP (https://www.ncbi.nlm.nih.gov/gap) because of patient privacy concerns.

first: Craig

last: Hersh


title: A mouse model featuring tissue specific deletion of p53 and Brca1 gives rise to mammary tumors with genomic and transcriptomic similarities to human basal-like breast cancer

first: Charles

last: Perou

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Single-cell RNA-sequencing of murine melanoma infiltrating immune cells in wild-type and miR-155 T cell conditional knockout mice

city: Holl

first: Ryan

last: O'Connell

state: UT

department: Pathology

institute: University of Utah

summary: miR-155 has recently emerged as an important promoter of antitumor immunity through its functions in T lymphocytes. However, the impact of T cell expressed miR-155 on immune cell  dynamics in solid tumors remains unclear. In the present study, we used single-cell RNA-sequencing to define the CD45+ immune cell populations within B16F10 murine melanoma tumors growing in either wild-type (WT) or miR-155 T cell conditional knockout (TCKO) mice at different timepoints. miR-155 was required for optimal T cell activation and reinforced the T cell response at the expense of infiltrating myeloid cells. Further, myeloid cells from tumors growing in TCKO mice were defined by an increase in wound healing genes and a decreased IFNg response gene signature. Finally, we found that miR-155 expression predicted a favorable outcome in human melanoma patients and was associated with a strong immune signature.  Moreover, gene expression and histological analysis of the Cancer Genome Atlas (TCGA) data revealed that miR-155 expression also correlates with an immune-enriched subtype in 29 other human solid tumor types. Together, our study provides an unprecedented analysis of the cell types and gene expression signatures by immune cells within experimental melanoma tumors and elucidates miR-155’s role in coordinating this dynamic response.

overall_design: B16F10 murine melanoma cells expressing ovalbumin model antigen were injected subcutaneously (1e6) into wild-type (C57BL/6) and miR-155 T cell conditional knockout mice (n>4). 9 or 12 days after injection, tumors were pooled in each group, and DAPI(-)CD45(+) live tumor infiltrating immune cells were sorted via flow cytometry. Sorted immune cells were processed for single-cell RNA-sequencing via 10x platform.

first: Thomas

last: Huffaker

first: H

last: Ekiz


title: A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees

city: Chicago

first: Michelle

middle: C

last: Ward

state: IL

address: 920 E. 58th Street, CLSC 317

department: Human Genetics

institute: University of Chicago

summary: Despite anatomical similarities, there are differences in susceptibility to cardiovascular disease (CVD) between primates; humans are prone to myocardial ischemia, while chimpanzees are prone to myocardial fibrosis. Induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) allow for direct inter-species comparisons of the gene regulatory response to CVD-relevant perturbations such as oxygen deprivation, a consequence of ischemia. To gain insight into the evolution of disease susceptibility, we characterized gene expression levels in iPSC-CMs in humans and chimpanzees, before and after hypoxia and re-oxygenation. The transcriptional response to hypoxia is generally conserved across species, yet we were able to identify hundreds of species-specific regulatory responses including in genes previously associated with CVD. The 1,920 genes that respond to hypoxia in both species are enriched for loss-of-function intolerant genes; but are depleted for expression quantitative trait loci and cardiovascular-related genes. Our results indicate that response to hypoxic stress is highly conserved in humans and chimpanzees.

sample_organism:
Pan troglodytes
Homo sapiens

platform_organism:
Pan troglodytes
Homo sapiens

overall_design: We collected RNA-seq data from iPSC-derived cardiomyocytes under normoxia (A), hypoxia (B), and two re-oxygenation time points (C & D) in eight human individuals (H) and seven chimpanzee individuals (C), together with technical replicates from three of the individuals in each species. Replicate samples are denoted with an 'R'.


title: Identification of Populus small RNAs responsive to mutualistic interactions with mycorrhizal fungi, Laccaria bicolor and Rhizophagus irregularis

city: Oak Ridge

first: Xiaohan

last: Yang

state: TN

address: 1 Bethel Valley Road

department: Biosciences Division

institute: Oak Ridge National Laboratory

type: Non-coding RNA profiling by high throughput sequencing

summary: Ecto- and endo-mycorrhizal colonization of Populus roots have a positive impact on the overall tree health and growth. A complete molecular understanding of these interactions will have important implications for increasing agricultural or forestry sustainability using plant:microbe-based strategies. These beneficial associations entail extensive morphological changes orchestrated by the genetic reprogramming in both organisms. In this study, we performed a comparative analysis of two Populus species (Populus deltoides and P. trichocarpa) that were colonized by either an arbuscular mycorrhizal fungus (AmF), Rhizophagus irregularis or an ectomycorrhizal fungus (EmF), Laccaria bicolor, to describe the small RNA (sRNA) landscape including small open reading frames (sORFs) and micro RNAs (miRNAs) involved in these mutualistic interactions. We identified differential expression of sRNAs that were, to a large extent, 1) within the genomic regions lacking annotated genes in the Populus genome and 2) distinct for each fungal interaction. These sRNAs may be a source of novel sORFs within a genome, and in this regard, we identified potential sORFs encoded by the sRNAs. We predicted a higher number of differentially-expressed miRNAs in P. trichocarpa (4 times more) than in P. deltoides (conserved and novel). In addition, 44 miRNAs were common in P. trichocarpa between the EmF and AmF treatments, and only 4 miRNAs were common in P. deltoides between the treatments.

sample_organism:
Populus trichocarpa
Populus deltoides

platform_organism:
Populus trichocarpa
Populus deltoides

overall_design: Examination of two Populus species (P. deltoides and P. trichocarpa) in response to either an arbuscular mycorrhizal fungus (Rhizophagus irregularis) or an ectomycorrhizal fungus (Laccaria bicolor)

first: Ritesh

last: Mewalal

first: Hengfu

last: Yin

first: Rongbin

last: Hu

first: Sara

last: Jawdy

first: Patrice

last: Vion

first: Gerald

last: Tuskan

first: François

last: Le Tacon

first: Jessy

middle: L

last: Labbé


title: Identification and development of DNA methylation biomarkers for oral/oropharyngeal cancers prevalent in the North-Eastern states of India

city: Shillong

first: Srimoyee

last: Ghosh

state: Meghalaya

address: Umshing-Mawkynroh

department: Zoology

country: India

institute: North Eastern Hill University

type: Methylation profiling by genome tiling array

summary: Whole-genome DNA methylation profiling of oral cancer in patients from North-Eastern states of India. The Illumina Infinium 450k Human DNA methylation BeadChip was used to screen the entire DNA methylation profiles across approximately 485,577 CpGs in matched oral cancer samples. Samples included 12 paired samples (12 cancer and 12 normal).

overall_design: Bisulphite-converted DNA from the 24 samples were hybridised to the Illumina Infinium 450k Human Methylation BeadChip.

first: Shngainlang

last: Khongsti


title: RNA-seq of Arabidopsis rosette cores

city: Richland

first: Hugh

last: Mitchell

state: Washington

address: 902 Battelle Blvd, P.O. Box 999, MSIN J4-18

department: Computational Biology

institute: Pacific Northwest National Laboratory

summary: The Arabidopsis rosette core can display full resistance against Botrytis cinerea. To reveal potential players in this resistance, the transcriptome of the Arabidopsis rosette core was determined.

overall_design: Identify transcriptome of Arabidopsis Col-0 rosette cores

first: Yanwan

last: Dai

first: Janet

last: Braam

first: Lye

last: Markillie

first: Matthew

last: Gaffrey

first: Galya

last: Orr


title: Chromatin remodeling mediated by ARID1A is indispensable for normal hematopoiesis in mice (ChIP-Seq)

first: Pushkar

last: Dakle

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Examination of H3K27Ac and H3K4me3 histone modifications in Lin- BM cells

first: Lin

last: Han

first: Vikas

last: Madan

first: Anand

last: Mayakonda

first: Weoi

last: Teoh

first: Pavithra

last: Shyamsunder

first: Hazimah

last: Nordin

first: Cao

last: Zeya

first: Janani

last: Sundaresan

first: Ienglam

last: Lei

first: Zhong

last: Wang

first: H

last: Koeffler


title: Gene Expression Changes Associated with Nintedanib Treatment in Idiopathic Pulmonary Fibrosis Fibroblasts

status: Public on Apr 08 2019

city: Kaohsiung

first: Wei An

last: Chang

address: No.100, Shihcyuan 1st Rd., Sanmin Dist., Kaohsiung City 80708, Taiwan (R.O.C.)

country: Taiwan

institute: Kaohsiung Medical University


title: Gene Expression Changes Associated with Nintedanib Treatment in Idiopathic Pulmonary Fibrosis Fibroblasts [miRNA-seq]

summary: We found strong protein-protein interactions within these dysregulated genes in nintedanib treated IPF fibroblast, with most genes involved in the pathways of cell cycle, mitotic cell cycle, and cell division. In IPF fibroblasts, we found nintedanib treatment was associated with downregulation of has-miR-92a-1-5p, which might de-repress SLC25A23 expression, and upregulation of has-miR-486-5p, which might repress DDX11, E2F1, and PLXNA4 expressions.

overall_design: Next-generation sequencing for mRNA and small RNA of IPF fibroblasts treated with nintedanib 2 μM and 4 μMnormal and without nintedanib

first: Chau-Chyun

last: Sheu

first: Wei-An

first: Po-Lin

last: Kuo

first: Ya-Ling

last: Hsu

first: Yi-Jen

last: Chen


title: Staphylococcus aureus drives expansion of low-density neutrophils in diabetic mice

city: Gaithersburg

first: Taylor

last: Cohen

state: MD

address: One Medimmune Way

institute: MedImmune

summary: Diabetes is associated with an increase in neutrophil NET production.  Low density neutrophils (LDNs) have a greater propensity for spontaneous production of NETs, and are increased in the diabetic host during infection with S. aureus.  We compared gene expression between high density (HDN) and LDNs isolated from the blood of infected db/db mice.

overall_design: Mice were infected with 5e7 CFU S. aureus (SF8300) and blood was collected 48h post infection.  Blood from 10 mice were pooled and LDNs and HDNs purified.  Matched pairs of LDN and HDN were compared.

first: Virginia

last: Takahashi

first: Jessica

last: Bonnell

first: Andrey

last: Tovchigrechko

first: Raghothama

last: Chaerkady

first: Wen

last: Yu

first: Omari

last: Jones-Nelson

first: Young

last: Lee

first: Rajiv

last: Raja

first: Kendall

last: Stover

first: Mark

last: Travis

first: Bret

last: Sellman


title: Transcriptional Down-regulation of CCR5 in a Subset of HIV+ Controllers (ATAC-Seq)

city: New Haven

first: Elena

last: Gonzalo Gil

state: Connecticut

address: 25 York street

institute: Yale University School of Medicine

summary: HIV+ Elite and Viremic controllers (EC/VCs) are able to control virus infection, perhaps because of host genetic determinants. We identified 16% (21 of 131) EC/VCs with CD4+ T cells with resistance specific to R5-tropic HIV, reversed after introduction of CCR5. R5 resistance was not observed in macrophages and depended upon the method of T cell activation. CD4+ T cells of these EC/VCs had lower CCR2 and CCR5 mRNA levels, reduced CCR2 and CCR5 cell-surface expression, and decreased levels of secreted chemokines. T cells had no changes in chemokine receptor mRNA half-life but instead had lower levels of active transcription of CCR2 and CCR5, despite having more accessible chromatin by Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq). Other nearby genes were also down-regulated, over a region of ~500kb on chromosome 3p21. This same R5 resistance phenotype was observed in family members of an index VC, also associated with CCR2/CCR5 down-regulation, suggesting that the phenotype is heritable.

overall_design: Examination of open Chromatin using ATACseq in activated CD4+ T cells from normal healthy controls and HIV elite controllers

last: Gonzalo-Gil

first: Patrick

last: Rapuano

first: Uchenna

last: Ikediobi

first: Rebecca

last: Leibowitz

first: Sameet

last: Mehta

first: Ayse

last: Coskun

first: J

middle: Z

last: Porterfield

first: Teagan

last: Lampkin

first: Vincent

last: Marconi

first: David

last: Rimland

first: Bruce

last: Walker

first: Steven

last: Deeks

first: Richard

last: Sutton


title: Estimating Genome-wide Off-Target Effects for Pyrrole-Imidazole Polyamide Binding by a Pathway-Based Expression Profiling Approach (ME180 cells)

first: Jason

last: Lin

summary: Side and off-target effects remain a difficult issue in the search of pharmaceutical leads, especially with DNA-binding molecules or genome editing methods where the issue becomes particularly thorny. A particular case is the investigations into the off-target effects of N-methylpyrrole-N-methylimidazole polyamides, a naturally inspired class of DNA binders that discriminately access the minor groove with strong affinity and sequence specificity but the relatively short motif of < 20 bases often imply possible non-unique genomic binding. Multiple binding sites may translate to binding at non-intended loci, potentially leading to off-target effects, issues that very few approaches are able to address to-date.  We here report an analytical method of inferring off-target binding from expression profiling based on the relative impact to various biochemical pathways, as well as an accompanying side effect prediction engine to allow candidate polyamides to be systematically screened. This method marks the first attempt in PI polyamide research to identify elements in various biochemical pathways sensitive to the treatment of a candidate polyamide to infer possible off-target effects. Expression changes were then considered for their possible effect on outward phenotypic changes, manifested as side effects, should the same PI polyamide candidate be administered clinically. We also performed a series of animal experiments to validate some of these effects, and found some corroboration in certain side effect manifestations, such as changes in the level of aspartate transaminase in ICR and nude mice after injection of some of the candidate polyamides in this study.

overall_design: O(4) to O(5) cells per condition were plated in a 6-well microtiter plate for overnight attachment prior to treatment of candidate polyamides or 0.05% DMSO. After RNA extraction with RNeasy Plus Mini Kit (Qiagen), labelled with RNA Spike-In Kit and analyzed on SurePrint G3 Human GE 8x60K V2 microarrays.

first: Sakthisri

last: Krishnamurthy

first: Takatori

last: Atsushi


title: Transcriptional Down-regulation of CCR5 in a Subset of HIV+ Controllers

last: Gonzalo Gil


title: Identification of a robust methylation classifier for cutaneous melanoma diagnosis

first: Nancy

last: Thomas

address: 405 Mary Ellen Jones Building

department: Dermatology

summary: Genome wide DNA methylation profiling of 89 primary invasive FFPE melanomas and 73 nevi were evaluated using the Illumina Infinium HumanMethylation450 BeadChip array

overall_design: Bisulfite converted DNAs from melanomas or nevi were hybridised to the Illumina Infinium HumanMethylation450 BeadChip

first: K

last: Conway


title: Estimating Genome-wide Off-Target Effects for Pyrrole-Imidazole Polyamide Binding by a Pathway-Based Expression Profiling Approach (SK-N-AS cells)

first: Hiroyuki

last: Yoda


title: Transcriptomic hallmarks of tumor plasticity and stromal interactions in brain metastasis [BrainMet_SQ_2D]

first: Don

last: Nguyen

state: CT

address: 310 Cedar St

institute: Yale Shcool of Medicine

summary: We find that malignant LUAD tumor cells grown in the brain microenvironment display significantly altered transcriptomic profiles when compared to tumor cells grown in monolayer or subcutaneously. Additionally, we characterize the reciprocal neuroinflammatory response of the surrounding brain stroma to metastatic LUAD. This dataset can be utilized to explore the mechanisms of LUAD cell plasticity as well as the co-adaptation of the brain microenvironment to metastatic disease.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Examination of the transcriptomic profiles of LUAD cells grown in different microenvironments (i.e., Brain, subcutaneous, monolayer culture) and the corresponding gene expression alterations of the stroma in the tumor-bearing brain.

first: Emily

last: Wingrove

first: Zongzhi

last: Liu

middle: X


title: Estimating Genome-wide Off-Target Effects for Pyrrole-Imidazole Polyamide Binding by a Pathway-Based Expression Profiling Approach

address: 666-2 Nitona-cho, Chuo-ku

institute: Chiba Cancer Center Research Institute


title: Single cell RNA sequencing identifies unique inflammatory airspace macrophage subsets

status: Public on Apr 07 2019

city: Denver

first: Nathan

last: Jackson

state: CO

address: 1400 Jackson St.

department: Center for Genes, Environment, and Health

institute: National Jewish Health

summary: In this study, we characterize transciprtional phenotypes of airway macrophagages (AMs) throughout homeostatsis, inflammation, and repair at single cell granularity. We confirm that cell origin is the major determinant of AM programing and describe two previously uncharacterized, transcriptionally distinct subdivisions of AMs based on proliferative capacity and inflammatory programing.

overall_design: We stimulated mice with LPS and then sampled FACs sorted airway macrophage cells using BAL at Days 0, 3, and 6 and sequenced 1,134 cells from these three groups using RNA-seq

first: Kara

last: Mould


title: A mouse model featuring tissue specific deletion of p53 and Brca1 gives rise to mammary tumors with genomic and transcriptomic similarities to human basal-like breast cancer [aCGH]

first: Charles

last: Perou

address: 12-044 Lineberger Comprehensive Cancer Center CB# 7295

institute: University of North Carolina at Chapel Hill

summary: In human basal-like breast cancer, mutations and deletions in TP53 and BRCA1 are frequent oncogenic events. Thus, we interbred mice expressing the CRE-recombinase with mice harboring loxP sites at TP53 and BRCA1 (K14-Cre; p53F/F Brca1F/F) to test the hypothesis that tissue specific deletion of TP53 and BRCA1 would give rise to tumors reflective of human basal-like breast cancer. In support of our hypothesis, these transgenic mice developed tumors that express basal-like cytokeratins and intrinsic gene expression features similar to human basal-like tumors. Array comparative genomic hybridization revealed a striking conservation of copy number alterations between the K14-Cre; p53F/F Brca1F/F mouse model and human basal-like breast cancer. Conserved events included MYC amplification, KRAS amplification, and RB1 loss. Microarray analysis demonstrated that these DNA copy number events also led to corresponding changes in signatures of pathway activation including high proliferation due to RB1 loss. K14-Cre; p53F/F Brca1F/F also matched human basal-like breast cancer for a proposentity to have immune-cell infiltrates. Given the long latency of K14-Cre; p53F/F Brca1F/F tumors (~250 days), we created tumor syngeneic transplant lines, as well as in vitro cell lines, which were tested for sensitivity to carboplatin and paclitaxel. These therapies invoked acute regression, extended overall survival, and resulted in gene expression signatures of an anti-tumor immune response. These findings demonstrate that this model is a valuable preclinical resource for the study of human basal-like breast cancer.

overall_design: 21 Agilent CGH microarrays were performed comparing DNA from mammary tumors to DNA from FVB wild-type mice.

first: Daniel

last: Hollern

first: Cristina

middle: M

last: Contreras

first: Stephanie

last: Dance-Barnes

first: Grace

last: Silva

first: Adam

last: Pfefferle

first: Jessie

last: Xiong

first: Kelly

last: Clark

last: Darr

first: Jerry

last: Usary

first: Kevin

last: Mott


title: Next Generation Sequencing Facilitates Quantitative Analysis of WT and dek42 mutant Transcriptomes

first: Yi

last: Zuo

address: No. 50 Road Zhanghua

institute: Beijing Academy of Agriculture and Forestry Science

summary: Analysis of gene expression level. The hypothesis tested in the present study was that dek42 mutant affects starch metabolism and pre-mRNA splicing.

overall_design: mRNA profiles of 15 DAP wild type (WT) and dek42 mutant were generated by deep sequencing, in triplicate, using Illumina Hiseq 2500 (Zea mays).

first: Rentao

last: Song


title: Temporal dynamic reorganization of 3D chromatin in hormone-induced breast cancer and endocrine resistance [T47D]

city: San Antonio

first: Yufan

last: Zhou

state: TX

address: 7703 Floyd Curl Dr

institute: UT health Science Center at San Antonio

summary: To establish a data-driven learning model of the temporal dynamics and 3D chromatin reorganization, we conducted tethered chromatin conformation (TCC) sequencing to examine 3D structure dynamics in estradiol (E2)-induced breast cancer T47D cells and Tamoxifen resistant breast cancer T47D cells.

overall_design: In this study, we conducted TCC analysis in hormone-starved T47D cells (T0) and compared this to T47D cells treated with 1hr of E2 (T1), 4hr of E2 (T4), 16hr of E2 (T16), 24hr of E2 (T24) and Tamoxifen resistant T47D cells. We could investigate dynamic 3D chromatin architecture in T47D cell lines from these TCC data.

first: Victor

last: Jin


title: Sequencing of freshly produced RNA following exposure of cells to DNA damage-inducing UV mimetic 4-hydroxyaminoquinolone (4-NQO)

city: München

first: Caroline

last: Friedel

address: Amalienstr. 17

department: Institut für Informatik

country: Germany

institute: Ludwig-Maximilians-Universität München

summary: We used Illumina-HiSeq4000 to sequence 4sU-labelled RNA samples isolated from unchallenged and DNA damaged HeLa Flp-In cells, which revealed the nature of transcriptional response folowing genotoxic stress and the contribution of P-TEFb kinase in DNA damage-induced gene transcription.

overall_design: We mock treated or treated HeLa Flp-In cells for 1 or 2 hr with DMSO, 4-NQO, or 4-NQO + flavopiridol (FP) as indicated below. During the last 30 minutes of the treatments, we labeled the RNA or not with the nucleoside analogue 4-thiouridine (500µM 4sU) for 30 minutes.

first: Andrii

last: Bugai

first: Alexandre

last: Quaresma

first: Tina

last: Lenasi

first: Christopher

last: Sibley

first: Petra

last: Kukanja

first: Koh

last: Fujinaga

first: Melanie

last: Blasius

first: Thomas

last: Hennig

first: Jernej

last: Ule

first: Lars

last: Dölken

first: Matjaz

last: Barboric


title: Gene expression data from LCMV-specific Rictor-/- and WT follicular T helper cells

city: Chongqing

first: Yifei

last: Wang

address: Gaotanya Street

department: Institute of Immunology

institute: Third Military Medical University

summary: Microarray experiments were performed to elucidate the transcriptome changes due to Rictor deficiency in  follicular T helper (TFH) cells. These data suggest TFH-lineage associated genes are down-regulated in Rictor-null TFH cells, indicating that Rictor primes TFH differentiation by regulating canonical genes of TFH cells.

overall_design: Rictor-null and WT TFH cells (2 samples per group, each sample was pooled from at least 5 mice) were sorted at day 8-post LCMV Armstrong infection, followed by total RNA extracted and sent to microarray analysis.

first: Lilin

last: Ye


title: Estimating Genome-wide Off-Target Effects for Pyrrole-Imidazole Polyamide Binding by a Pathway-Based Expression Profiling Approach (CaSki cells)

city: Chiba

first: Jason

last: Lin

first: Sakthisri

last: Krishnamurthy

first: Takatori

last: Atsushi


title: Identification of novel neuroprotective loci modulating ischemic stroke volume in a cross between wild-derived inbred mouse strains

status: Public on Apr 06 2019

city: Durham

first: Douglas

last: Marchuk

address: 213 Research Drive

department: Molecular Genetics and Microbiology

institute: Duke University

summary: We employed RNA-sequencing to identify differentially expressed genes between two wild-derived inbred mouse strains. These strains exhibit high collateral blood vessel densities, but differ in widely in infarct volume following middle artery occlusion. This experiment helped facilitate identification of candidate loci underlying this differential response.

overall_design: Examination of differentially expressed genes between strains which exhibit differential infarct volumes after middle artery occlusion

first: Han

last: Lee

first: Samuel

last: Widmayer

first: David

last: Aylor


title: Estimating Genome-wide Off-Target Effects for Pyrrole-Imidazole Polyamide Binding by a Pathway-Based Expression Profiling Approach (MC-IXC cells)

first: Hiroyuki

last: Yoda


title: Gene expression profiles of Foxp3RFP (WT), Foxp3∆EGFPiCre (Foxp3-deficient) and Foxp3∆EGFPiCreRictor∆/∆ (Foxp3-deficient and Rictor deficient) Treg cells.

city: Los Angeles

first: Feiyang

last: Ma

state: CA

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

summary: Comparaison of the transcriptomes of WT and Foxp3-deficient regulatory T cells from the spleen of  females that carried one mutant Foxp3∆EGFPiCre allele and a second competent Foxp3 allele (Foxp3RFP) that also directed the expression of the red fluorescent protein (RFP) . We then extended these studies to elucidate transcriptional pathways altered upon Rictor deletion in ∆Treg cells that may contribute to their improved regulatory function by analyzing the transcriptome of ∆Treg cells isolated from Foxp3∆EGFPiCre/+Rictor∆/∆ females.

overall_design: Splenic Treg (CD4+RFP+ or CD4+YFP+) cells were double-sorted from 4 weeks old female Foxp3∆EGFPiCre/RFPR26YFP and Foxp3∆EGFPiCre/+Rictor∆/∆R26YFP mice. (n=4 per group). Cells were collected directly into TRIzol (Invitrogen). Total RNA was extracted and converted into double-stranded DNA (dsDNA), using SMART-Seq v4 Ultra Low Input RNA kit (Clontech). dsDNA was then fragmented to 200- to 300-bp-sized fragments, using M220 Focused-ultrasonicator (Covaris), and these were used for the construction of libraries for Illumina sequencing, using the KAPA Hyper Prep Kit (Kapa Biosystems). Libraries were then quantified using Qubit dsDNA HS (high-sensitivity) Assay Kit on Agilent High Sensitivity DNA Bioanalyzer. RNA sequencing data was demultiplexed by using perfect matches to indices and was quality-inspected using FastQC. The sequencing data was aligned to the mm10 build (Gencode annotation) of the mouse genome using STAR, and counts were quantified using HTSeq-Counts.

first: Louis-Marie

last: Charbonnier

first: Matteo

last: Pellegrini

first: Talal

last: Chatila


title: Estimating Genome-wide Off-Target Effects for Pyrrole-Imidazole Polyamide Binding by a Pathway-Based Expression Profiling Approach (Kelly cells)


title: Gene Expression Changes Associated with Nintedanib Treatment in Idiopathic Pulmonary Fibrosis Fibroblasts [RNA-seq]

first: Wei An

last: Chang

overall_design: Next-generation sequencing for mRNA and small RNA of IPF fibroblasts treated with nintedanib 2 μM and 4 μM normal and without nintedanib

first: Chau-Chyun

last: Sheu

first: Wei-An

first: Po-Lin

last: Kuo

first: Ya-Ling

last: Hsu

first: Yi-Jen

last: Chen


title: Flg22 induces CERK1 phosphorylation

city: Guangzhou

first: Ben-Qiang

last: Gong

state: Guangdong

address: No. 135, Xingang Xi Road, Guangzhou

department: School of Life Sciences

institute: Sun Yat-sen University

summary: Plant cells employ cell-surface receptors to detect pathogens and launch immunity.Here we show that flg22 can induce a receptor-like kinase CERK1 phosphorylation at juxtamembrane region (JM). However, Genome-wide transcriptional reprogramming and other flg22 responses implied that CERK1 does not directly mediate flg22 signaling. Surprisingly, CERK1 JM phosphorylation can promote chitin responses and fungal resistance for plants and genome-wide transcriptional reprogramming also suggested no sign of constitutive immunity caused by this.

overall_design: Genome-wide survey of the wild type and cerk1 mutant in response to flg22 or transgenic complementation plants of CERK1 and CERK1 mutations

first: Nannan

last: Zhang

first: Jianhang

last: Guo

first: Xinran

last: Yao

first: Hong-Bin

last: Wang

first: Jian-Feng

last: Li


title: Temporal dynamic reorganization of 3D chromatin in hormone-induced breast cancer and endocrine resistance

first: Yufan

last: Zhou

summary: To establish a data-driven learning model of the temporal dynamics and 3D chromatin reorganization, we conducted tethered chromatin conformation (TCC) sequencing to examine 3D structure dynamics in estradiol (E2)-induced breast cancer MCF7 cells and Tamoxifen resistant breast cancer MCF7 cells.

overall_design: In this study, we conducted TCC analysis in hormone-starved MCF7 cells (T0) and compared this to MCF7 cells treated with 1hr of E2 (T1), 4hr of E2 (T4), 16hr of E2 (T16), 24hr of E2 (T24) and Tamoxifen resistant MCF7 cells. We integrated next generation 3D chromatin sequencing data with ChIP-seq data of histone marks H3K4me1, H3K4me3, H3K27ac, H3K9me3, and H3K27me3 and gene expression data.

first: Victor

last: Jin


title: The CCCTC binding factor, CTRL2, controls heterochromatin deposition and the establishment of HSV-1 latency in vivo

status: Public on Apr 05 2019

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

institute: University of Vermont

summary: The cellular insulator  CCCTC-binding factor (CTCF) plays a role in HSV-1 latency through the establishment of chromatin boundaries. We previously found that the CTRL2 regulatory element downstream from the LAT enhancer  is bound by CTCF during latency and undergoes CTCF eviction at early times post-reactivation in mice latent with 17Syn+ . It has been previously shown that the CTRL2 binding domain is a functional insulator with both enhancer-blocking and silencing capabilities. Considering these findings, we hypothesized that the CTRL2 site plays a key role in regulating latent HSV-1 gene expression. To test this, we used a mutant virus with a 135 bp deletion spanning only the core CTRL2 domain (DCTRL2) in the 17Syn+ background. Following ocular infection of mice, we found significant differences between DCTRL2 and wild-type virus during the acute infection and latency. Notably, mouse mortalities were significantly higher in the DCTRL2 virus compared to the 17Syn+, while lower viral genomes were found after latency indicating that deletion of CTRL2 site disrupted latency establishment.  This fact, coupled with increased LAT intron and VP16 expression indicated that the establishment of latency was disrupted in the DCTRL2 mutant. These data provide evidence that chromatin domains of the latent HSV-1 genome are in part maintained by the CTRL2 binding.

overall_design: 4-6 weeks of age BALB/c mice were anesthetized using intramuscular injections of ketamine and xylazine infected with 2 different strains of HSV1 (WT and DeltaCTRL2) in the corneal epithelium. (ChIP-seq) was performed using trigeminal ganglia (TG) from three mice.

first: Mike

last: Mariani


title: Transcriptomic hallmarks of tumor plasticity and stromal interactions in brain metastasis [MultiDisease]

first: Don

last: Nguyen

summary: We report that well-defined xenograft models of leading sources of CNS metastasis (melanoma, breast cancer, lung cancer) undergo specific transcriptomic alterations upon entering the brain microenvironment. This dataset can be utilized to explore the mechanisms of tumor cell plasticity as well as the co-adaptation of the brain microenvironment to metastatic disease.

overall_design: Examination of the transcriptomic profiles of lung cancer, breast cancer, and melanoma models of brain metastatic disease and the resulting gene expression changes of the stroma in the tumor-bearing brain.

first: Emily

last: Wingrove

first: Zongzhi

last: Liu


title: Identification of the genes under the control of  the transcription factor Prdm12 in  somatosensory neurons

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

summary: Prdm12, a novel key regulator of the Nerve Growth Factor-TrkA signaling pathway, is required for nociceptive sensory neuron development

overall_design: RNA-seq analysis in triplcate of the transcriptome of thoracic dorsal root ganglia with associated  spinal cord of E11.5 Prdm12 KO and WT embryos.

first: Simon

last: Desiderio

last: Vermeiren


title: Hair growth is induced by blockade of macrophage-derived oncostatin M and JAK-STAT5 signaling in hair follicle stem cells.

city: New York City

first: Etienne

state: NY

address: 1150 St Nicholas Avenue, Room 303

institute: Columbia University

summary: We also show that OSM is sufficient for maintaining quiescence of hair follicle stem cells (HFSCs), and OSMRβ-JAK-STAT5 signaling is necessary for maintaining the resting phase of the hair cycle (telogen). Using single-cell RNA sequencing, we identify the source of OSM to be a distinct subset of TREM2+ macrophages that predominate during early telogen. Moreover, inhibition of macrophages during telogen by genetic ablation, neutralizing antibodies and small-molecule inhibitors was sufficient to induce anagen.

overall_design: Single-cell RNA sequencing of CD45+ immune cells at 4 timepoints during murine telogen.

first: Angela

last: Christiano


title: Local restriction of sterile inflammation by auto-inhibitory regulation of S100A8/S100A9-alarmin activity

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Autoimmune diseases, like psoriasis or arthritis, show a patchy distribution of inflammation despite systemic dysregulation of adaptive immunity. Thus, additional tissue-derived signals like Danger-Associated Molecular Pattern molecules (DAMPs) are indispensable for manifestation of local inflammation. S100A8/100A9-complexes are the most abundant DAMPs in many autoimmune diseases. However, regulatory mechanisms locally restricting DAMP-activities are barely understood. We now unravel for the first time a novel mechanism of auto-inhibition in mice and man restricting S100-DAMP activity to local sites of inflammation. Combining protease degradation, pull-down assays, mass spectrometry and targeted mutations we identified specific peptide sequences within the second calcium-binding EF-hands triggering TLR4/MD2-dependent inflammation. These binding sites are free when S100A8/S100A9-heterodimers are released at sites of inflammation. Subsequently, S100A8/S100A9-activities are locally restricted by calcium-induced (S100A8/S100A9)2-tetramer formation now hiding the TLR4/MD2-binding site within the tetramer interphase thus preventing undesirable systemic effects. Loss of this auto-inhibitory mechanism in vivo results in TNFa-driven fatal inflammation as shown by lack of tetramer formation crossing S100A9-/- mice with two independent TNFa-transgene mouse strains. Since S100A8/S100A9 is the most abundant DAMP in many inflammatory diseases, specifically blocking of the TLR4-binding site of active S100-dimers represents an innovative approach for local suppression of inflammatory diseases avoiding systemic side effects.

overall_design: Human blood monocytes stimulated with MRP8 (S100A8) - MRP14 (S100A9) homo or hetero dimers or LPS were used for RNA extraction and hybridization on Illumina microarrays.

first: Thomas

last: Vogl

first: Athanasios

last: Stratis

first: Viktor

last: Wixler

first: Tom

last: Völler

first: Sumita

last: Thurainayagam

first: Selina

last: Jorch

first: Stefanie

last: Zenker

first: Alena

last: Dreilung

first: Deblina

last: Chakraborty

first: Mareike

last: Fröhling

first: Peter

last: Paruzel

first: Corinna

last: Wehmeyer

first: Sven

last: Hermann

first: Olympia

last: Papantonopoulou

first: Christiane

last: Geyer

first: Karin

last: Loser

first: Michael

last: Schafers

first: Stephan

last: Ludwig

first: Monika

last: Stoll

first: Tomas

last: Leanderson

first: Simone

last: König

last: Pap

first: Johannes

last: Roth


title: Cooperative adaptation to therapy (CAT) confers resistance in heterogeneous non-small cell lung cancer

city: Cambridge

first: Aaron

last: Goldman

state: MA

address: 65 Landsdowne St.

institute: mitra biotech

summary:
To study the interaction between mutated clones using interspecies competition and mathematical models
Methods: RNA was extracted from 3-D cultures after 48 hours of growth in spheroids using manufacturer protocol (Qiagen) and sequenced in duplicate using Illumina NextSeq500. libraries were prepared from 500ng of purified RNA using Illumina TruSeq preparation kits.  Sequence reads that passed quality filters were aligned to the UCSC mm9 reference genome and quanitifed using STAR (v2.5.1b). Normalized read counts (FPKM) were calculated using cufflinks and transcriptome profiling was analyzed using DESeq2.
We determined that previously sensitive cancer cell clones within heterogeneous tumors will induce drug resistant phenotypes among neighboring cells while under drug pressure
Non-mutational drug resistance can arise through drug-induced mechanisms augmented in heterogeneous tumors.

overall_design: Wild-type and Dicer1-mutated cell lines were analyzed for transcriptomic variation by RNA sequencing using Illumina NextSeq500.


title: Cerebral Cavernous Malformation Proteins and MEKK3 Coordinately Modulate SMURF1 Abundance to Control RhoA-dependent Endothelial Cell Phenotypic State

city: Chapel Hill

first: Adriana

middle: Sujey

last: Beltran

address: 120 Mason farm Rd

department: Pharmacology

institute: UNC-CH

summary: Cerebral Cavernous Malformations (CCM), caused by loss of CCM1, CCM2 or CCM3 in endothelial cells (ECs), are leaky capillaries causing seizures and stroke. CCM protein loss gives overlapping changes in biomechanical and transcriptional properties of ECs, due to common RhoA-driven alterations in cytoskeletal organization and intracellular signaling. However, EC models of 3-D tube formation show loss of each CCM protein generates distinct morphological defects in tubular structures. Computational modeling, live-cell imaging and RNA sequencing revealed distinct functional roles of CCM1 and CCM3 in regulating EC-EC and EC-matrix interactions. CCM2 has an intermediate phenotype consistent with its interaction with CCM1 and CCM3. In ECs, CCM proteins regulate SMURF1 E3 ligase ubiquitination and degradation of RhoA. Loss of CCM proteins results in loss of SMURF1 and a concomitant increase of MEKK3, a negative regulator of SMURF1 expression. We propose CCM lesions develop because of dysregulated SMURF1 resulting in RhoA and MEKK3 gain-of-function.

overall_design: 29 experimental samples with replicates indicated in sample title

first: Gary

last: Johnson


title: lncRNA expression analysis in patients with eosinophilic and neutrophilic asthma

city: Beijing

first: Yu-Jin

last: Zhu

address: FuXing Road, Haidian District

institute: Chinese PLA General Hospital

summary: Long non-coding RNA (lncRNA) are known to be important in many diseases. There has been some reports that lncRNA take part in the pathogenesis of systemic inflammation of asthma. lncRNA regulates gene transcription, protein expression and epigenetic regulation. However, the lncRNAs associated with differently airway phenotype such as eosinophilic and neutrophilic asthma remains unknown.  We aimed at identifying the differences in circulating lncRNA signature in Eos and Neu samples. lncRNA expression were studied between blood samples from Eos patients, Neu patients and healthy individuals (Control). Bioinformatic analysis was used to describe relevant biological pathways. Using quantitative real-time PCR, lncRNA expression was measured.   Comparing with Control samples, Eos sample has 190 own lncRNA and Neu sample has 166 own lncRNA(difference ≥ 2-fold).  KEGG pathway annotation data and GO terms revealed that several lncRNAs are possibly associated with respective phenotype. lncRNA was identifying  to differ significantly between Eos and Neu samples by using qRT-PCR.  The results show us that lncRNA may be involved in different phenotypes of asthma. Whether we can recognize different phenotypes of asthma through these lncRNA (as biomarkers) needs further study.

overall_design:
Patients with eosinophilic asthma  (Eos, n = 12) and neutrophilic asthma  (Neu, n = 6) were selected in the study according the accepted standard (Eos: induced sputum eosinophil count >3% and neutrophils <63%; Neu: induced sputum eosinophil count <3% and neutrophils>63% )1. Exclusion criteria contained recent (within the past weeks) respiratory tract infection, recent unstable asthma, recent asthma exacerbation, current smoking (or a history of smoking, within 6 months of cessation), and changes in maintenance therapy. All participants were selected from the People’s Liberation Army General Hospital, and all participants have been given informed consent before their inclusion. Healthy individuals were selected as Control samples (n = 6).
The results show us that lncRNA may be involved in different phenotypes of asthma. Whether we can recognize different phenotypes of asthma through these lncRNA (as biomarkers) needs further study.
This dataset is related to GSE106230

first: Y


title: Transcriptomic hallmarks of tumor plasticity and stromal interactions in brain metastasis [BrainMet_Othotopic]

first: Don

last: Nguyen

address: 310 Cedar St

institute: Yale Shcool of Medicine

summary: We find that malignant LUAD tumor cells grown in the brain microenvironment display significantly altered transcriptomic profiles when compared to tumor cells grown in monolayer or subcutaneously. Additionally, we characterize the reciprocal neuroinflammatory response of the surrounding brain stroma to metastatic LUAD. This dataset can be utilized to explore the mechanisms of LUAD cell plasticity as well as the co-adaptation of the brain microenvironment to metastatic disease.

overall_design: Examination of the transcriptomic profiles of LUAD cells grown in different microenvironments (i.e., brain or lung) and the corresponding gene expression changes of the stroma in the tumor-bearing brain.

first: Emily

last: Wingrove

first: Zongzhi

last: Liu

first: Manuel

last: Valiente


title: Genome-wide profiles of chromatin accessibility in spatially-restricted domains along the antero-posterior axis of Drosophila blastoderm

status: Public on Apr 04 2019

city: Planegg-Martinsried

first: Nicolas

last: Gompel

address: Grosshaderner Strasse 2

department: Faculty of Biology, Biozentrum

institute: Ludwig Maximilian University of Munich (LMU)

summary: Establishment of spatial coordinates during early Drosophila embryogenesis relies on differential activity of axis patterning enhancers. Concentration gradients along the embryonic axes of activator and repressor transcription factors (TFs) provide positional information to each enhancer, which in turn promotes transcription of a target gene in a specific spatial pattern. In order to receive the TF input, an enhancer must be accessible. However, the interplay between an enhancer regulatory activity and its accessibility as determined by local chromatin organization in not well understood. Notably, it is unclear whether chromatin organization of axis patterning enhancers is uniform across the embryo or varies regionally with their differential activity. We profiled chromatin accessibility with ATAC-seq in narrow, genetically tagged domains along the antero-posterior (AP) axis in the Drosophila blastoderm. In a series of transgenic strains, we drove expression of a nuclear tag (nuclear-envelope marker UNC84-3xFLAG) under control of well-characterised enhancers of the AP gene regulatory network. Tagged nuclei were subsequently isolated from the whole-embryo homogenate by anti-FLAG antibody pull-down, followed by Tn5 transposase digestion of the native chromatin (ATAC-seq). We demonstrate that one quarter of the accessible genome displays significant regional variation in its ATAC-seq signal immediately after zygotic genome activation. Axis patterning enhancers are enriched among the most variable regions and their accessibility changes correlate with their regulatory activity. When receiving a net activating input and promoting transcription, an enhancer displays elevated accessibility in comparison to the region of the embryo where it receives a net repressive input.

overall_design: ATAC-seq was performed on tagged nuclei from seven domains (D1-D7) along the AP axis of stage-5 Drosophila melanogaster blastoderm. Spatial positions of these domains were defined by expression of a nuclear tag under control of well-characterized enhancers of early blastoderm genes (D1: hunchback anterior domain; D2: even-skipped stripe 2; D3: even-skipped stripe 1; D4: Dichaete central domain; D5: Kruppel central domain; D6: even-skipped stripe 5; D7: giant posterior domain). All transgenic strains were generated in the wild-type background. Each domain was assayed in duplicates that represented independent transgenic strains with the same expression construct. As a control, ATAC-seq was performed on the entire pool of nuclei from selected transgenic strains (referred to as whole-embryo controls; performed in duplicates). Additionally, ATAC-seq performed on purified genomic DNA was used as a reference for peak calling (gDNA sample).

first: M

last: Bozek

first: R

last: Cortini

first: A

last: Storti

first: U

last: Unnerstall

last: Gaul

first: N


title: Phloem-related genes are downregulated during radial growth of smxl4 smxl5 double mutant stems

city: Heidelberg

first: Thomas

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

institute: Heidelberg University

summary: As a prerequisite for constant growth, plants can produce vascular tissues at different sites in their postembryonic body. In particular, the formation of vascular tissues during longitudinal and radial expansion of growth axes differs fundamentally with respect to its anatomical configuration. This raises the question to which level regulatory mechanisms of vascular tissue formation are shared throughout plant development. Here, we show that, similar as primary phloem formation during longitudinal growth, the cambium-based formation of secondary phloem depends on the function of SMXL genes. Using promoter reporter lines, we observe that SMXL4 and SMXL5 activities are associated with different stages of secondary phloem formation in Arabidopsis stems and that specific loss of SMXL5 function results in the absence of secondary phloem. Interestingly, the additional disruption of SMXL4 activity increases cell proliferation rates in the cambium region without forming secondary phloem. Based on genome-wide transcriptional profiling and expression analyses of phloem-related markers we conclude that early steps of phloem formation are impaired in smxl4;smxl5 double mutants and that additional cambium-derived cells fail in establishing any phloem-related feature. Our results show that molecular mechanisms determining primary and secondary phloem share important features but differ slightly with SMXL5 playing a more dominant role in the formation of secondary phloem.

overall_design: We compared the transcriptomes of Arabidopsis thaliana stem bases displaying radial growth between phloem-defective smxl4 smxl5 double mutants and wild type.

first: Eva-Sophie

last: Wallner

first: Virginie

last: Jouannet


title: Engineering a haematopoietic stem cell niche by reprogramming mesenchymal stromal cells (ATAC-Seq)

city: Bronx

first: Fumio

last: Nakahara

address: 1301 Morris Park Ave., Price Center Rm. 107

department: Dep. of Cell Biology

institute: Albert Einstein College of Medicine

summary: Haematopoietic stem cells (HSCs) reside in bone marrow (BM) niches where they are maintained to replenish all blood cell lineages throughout life. Among the constituents of the murine HSC niches, various cell types such as CXCL12-abundant reticular (CAR) cells, Nestin-GFP+ perivascular cells, leptin receptor (LepR)+ cells, endothelial cells, osteoblasts, sympathetic nerves, macrophages and megakaryocytes in the BM have been proposed to contribute to HSC niche activity. When niche cells are removed from their natural habitat, the ability to maintain HSCs ex vivo is markedly diminished. Mesenchymal-derived stromal cells (MSCs) identified by Nestin-GFP express high levels of niche factors in vivo, but their expression is downregulated rapidly upon culture, suggesting that alterations in transcriptional rewiring may contribute to the reduced HSC maintenance potential. We found that the enforced expression of 5 genes (Klf7, Ostf1, Xbp1, Irf3 and Irf7) markedly restored HSC niche function in cultured BM-derived MSCs. These revitalized MSCs (rMSCs) exhibited boosted synthesis of HSC niche factors while retaining their mesenchymal lineage differentiation capacity. By contrast to HSCs co-cultured with control MSCs, HSCs expanded with rMSCs showed significantly higher repopulation capacity. To evaluate to what extent rMSCs are reprogrammed toward freshly isolated MSCs, we compared, by RNA-seq analysis, the transcriptome of freshly sorted CD45(-) Ter119(-) CD31(-) Scf-GFP(-) cells, CD45(-) Ter119(-) CD31(-) Scf-GFP(+) cells, rMSCs and control vector-transduced stroma. HSC niche-associated genes were highly expressed in both native Scf-GFP(+) stromal cells and rMSCs compared to the Scf-GFP cell fraction and control MSCs. With the motif analysis of ATAC-seq data, we found that myocyte enhancer factor 2c (Mef2c) is one of the key factor in the revitalization of MSCs. These results suggest that rMSC may provide a promising platform for curative transplantation therapies.

overall_design: Examination of 4 different cell types; freshly sorted CD45(-) Ter119(-) CD31(-) Scf-GFP(-) cells (n=2), CD45(-) Ter119(-) CD31(-) Scf-GFP(+) cells (n=2), rMSCs (n=3) and control vector-transduced stroma (n=3).

first: Paul

last: Frenette

first: John

last: Greally

first: Masako

last: Suzuki


title: NOTCH3-IC

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

country: Netherlands

institute: msterdam UMC and University of Amsterdam

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

overall_design: Refer to individual Series


title: Reversible induction NOTCH3-IC in SH-SY5Y.

summary: Expression analysis of ADRN cell line SH-SY5Y with transient- or permanent doxycycline-inducible NOTCH3-IC expression was used to study reversibility of transcriptional reprogramming.

overall_design: Cells were induced with doxycycline for 7 or 14 days to analyze mRNA. Transient induction with doxycycline for 7 days was followed by 7 days off doxycycline to study reversibility of NOTCH3-IC-induced transcriptome.

first: Johan

last: van Nes


title: Transcriptomic hallmarks of tumor plasticity and stromal interactions in brain metastasis

city: New Haven

first: Don

last: Nguyen


title: Expression data from adipose stromal cells

city: toulouse

first: Amandine

last: GIROUSSE

address: 4 bis avenue Hubert Curien, Bâtiment INCERE stromalab

country: France

institute: CNRS

summary:
Adipose stromal cells are adipocytes progenitors lying in the stroma vascular fraction of adipose tissue. They can also be released into the circulation upon dietary challenges.
We used microarrays to compare the global programme of gene expression between adipose stromal cells originating from murine subcutaneous and perigonadal adipose depots

overall_design: Adipose stromal cells (ASCs) were isolated from either subcutaneous or perigonadal adipose depots from 6 animals and pooled by tissue origin. 3 independant pools of ASCs were done per tissue type.

first: Emmanuelle

last: Arnaud

first: Coralie

last: Sengenès


title: Antidepressants affect gut microbiota and Ruminococcus flavefaciens is able to abolish their effects on depressive-like behavior

city: Sefad

first: Evan

last: Elliott

state: - Select a State -

address: Henrieta Sold 8

country: Israel

institute: Bar Ilan University

summary: Accumulating evidence demonstrates that the gut microbiota affects brain function and behavior, including depressive behavior. Antidepressants are the main drugs used for treatment of depression. We hypothesized that antidepressant treatment could modify gut microbiota which can partially mediate their antidepressant effects. Mice were chronically treated with one of five antidepressants (fluoxetine, escitalopram, venlafaxine, duloxetine or desipramine), and gut microbiota was analyzed, using 16s rRNA gene sequencing. After characterization of differences in the microbiota, chosen bacterial species were supplemented to vehicle and antidepressant-treated mice, and depressive-like behavior was assessed to determine bacterial effects. RNA-seq analysis was performed to determine effects of bacterial treatment in the brain. Antidepressants reduced richness and increased beta diversity of gut bacteria, compared to controls. At the genus level, antidepressants reduced abundances of Ruminococcus, Adlercreutzia, and an unclassified Alphaproteobacteria. To examine implications of the dysregulated bacteria, we chose one of antidepressants (duloxetine) and investigated if its antidepressive effects can be attenuated by simultaneous treatment with Ruminococcus flavefaciens or Adlercreutzia equolifaciens. Supplementation with R. flavefaciens diminished duloxetine-induced decrease in depressive-like behavior, while A. equolifaciens had no such effect. R. flavefaciens treatment induced changes in cortical gene expression, up-regulating genes involved in mitochondrial oxidative phosphorylation, while down-regulating genes involved in neuronal plasticity. Our results demonstrate that various types of antidepressants alter gut microbiota composition, and further implicate a role for R. flavefaciens in alleviating depressive-like behavior.

overall_design: Examination of whole genome transcription in frontal cortex of mice treated with duloxetine with/without R. flavefaciens treatment

first: Iva

last: Lukic


title: Transcriptional Down-regulation of CCR5 in a Subset of HIV+ Controllers (RNA-Seq)

first: Elena

last: Gonzalo Gil

address: 25 York street

institute: Yale University School of Medicine

summary: HIV+ Elite and Viremic controllers (EC/VCs) are able to control virus infection, perhaps because of host genetic determinants. We identified 16% (21 of 131) EC/VCs with CD4+ T cells with resistance specific to R5-tropic HIV, reversed after introduction of CCR5. R5 resistance was not observed in macrophages and depended upon the method of T cell activation. CD4+ T cells of these EC/VCs had lower CCR2 and CCR5 mRNA levels, reduced CCR2 and CCR5 cell-surface expression, and decreased levels of secreted chemokines. T cells had no changes in chemokine receptor mRNA half-life but instead had lower levels of active transcription of CCR2 and CCR5, despite having more accessible chromatin by Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq). Other nearby genes were also down-regulated, over a region of ~500kb on chromosome 3p21. This same R5 resistance phenotype was observed in family members of an index VC, also associated with CCR2/CCR5 down-regulation, suggesting that the phenotype is heritable.

overall_design: RNA-seq was performed to identify up- or down-regulated genes associated with in vitro resistance to R5-tropic viruses in activated CD4+ T cells from HIV+ Elite Controllers and family members

last: Gonzalo-Gil

first: Patrick

last: Rapuano

first: Uchenna

last: Ikediobi

first: Rebecca

last: Leibowitz

first: Sameet

last: Mehta

first: Ayse

middle: K

last: Coskun

first: J

last: Porterfield

first: Teagan

last: Lampkin

first: Vincent

last: Marconi

first: David

last: Rimland

first: Bruce

last: Walker

first: Steven

last: Deeks

last: Sutton


title: Functional proteomics identified an upstream trancription complex promoting piRNA biogenesis

city: cambridge

first: Eric

last: Miska

address: tennis court road

department: The Gurdon Institute

country: United Kingdom

institute: University of Cambridge

summary: Here we used functional proteomics approaches to identify an upstream transcription complex (USTC) that is required for piRNA biogenesis. The complex contains PRDE-1, SNPC-4, TOFU-4, and TOFU-5, all of which are enriched on the two piRNA clusters on chromosome IV and form distinct piRNA foci in the nucleus.

overall_design: Examination of functional role of a newly discovered complex in piRNA biogenesis

first: Julie

last: Ahringer

first: Shouhong

last: Guang


title: TCR density in early iNKT cell precursors regulates agonist selection and subset differentiation in mice

status: Public on Apr 03 2019

city: Paris

first: Marc

last: Delord

address: Hopital Saint-Louis, 1 avenue Claude Vellefaux

department: Recherche clinique

institute: Centre hospitalier de Versailles

summary: We address the question of the nature of the signal perceived by iNKT cells promoting their specification, we analyzed iNKT cell development in relevant TCR Vα14-Jα18 alpha chain transgenic mice (Vα14Tg)

overall_design: We investigate the transcriptional difference of iNKT cells between CD4-Vα14Tg mice, where the transgene is driven by CD4 promoter vs WT controls

first: C

last: Joseph

last: Klibi

first: L

last: Amable

last: Comba

first: A

last: Cascioferro

first: M

first: V

last: Parietti

last: Lenoir

first: S

last: Latour

first: B

last: Lucas

last: Viret

last: Toubert

first: K

last: Benlagha


title: Urinary exosome miR-30c-5p as a biomarker of clear cell renal cell carcinoma that inhibits progression by targeting HSPA5

city: Shanghai

first: Chong

last: Wang

address: Gangao Road 271

institute: Shanghai Liangrun

summary: Exosome-derived miRNAs are regarded as biomarkers for the diagnosis and prognosis of many human cancers. However, its function in clear cell renal cell carcinoma (ccRCC) remains unclear. In this study, differentially expressed miRNAs from urinal exosomes were identified using next-generation sequencing (NGS) and verified using urine samples of ccRCC patients and healthy donors. Then the exosomes were analyzed in early-stage ccRCC patients, healthy individuals and patients suffering with other urinary system cancers. Afterwards, the target gene of the miRNA was detected. Its biological function was investigated in vitro and in vivo. The results showed that miR-30c-5p could be stably amplified. Its expression pattern was significantly different only between ccRCC patients and healthy control individuals, but not compared with that of other urinary system cancers, which indicated its ccRCC specificity. Additionally, the overexpression of miR-30c-5p inhibited ccRCC progression in vitro and in vivo. Heat shock Protein 5 (HSPA5) was found to be a direct target gene of miR-30c-5p. HSPA5 depletion caused by miR-30c-5p inhibition reversed the promoting effect of ccRCC growth. In conclusion, urinary exosomal miR-30c-5p acts as a potential diagnostic biomarker of early-stage ccRCC, and might modulate the expression of HSPA5, which is correlated with the progression of ccRCC.

overall_design: To study the expression pattern of exosomal miRNA in the samples from ccRCC patients and healthy control individuals, total RNA was first isolated from the urine exosomes. The contents of small RNAs in the exosomes of ccRCC patients and healthy control individuals were consistent. Afterwards, miRNAs were isolated from total RNA and next-generation sequencing (NGS) was performed to compare the urinary exosome miRNA expression pattern of ccRCC patients with that of healthy individuals. The samples were then analyzed using an ultra-sequencer Illumina HiSeq2500, a platform that can deliver high quality data. After quality controls and adapter elimination, only high quality reads were aligned using a mirDeep2 algorithm against the mirBase v21 database, for the identification and quantification of previously described miRNAs. In total, 126 miRNA species were identified.

first: Shangqing

last: Song

first: Yajun

last: Cheng

first: Guopeng

last: Yu

first: Qing

last: Yang

first: Jiayi

last: Liu

first: YiWei

first: Jiayan

last: Sheng

first: Linhui

first: Zhong

first: Bin

last: Xu


title: Topoisomerase VI participates to a chromatin barrier-like function that prevents heterochromatin spreading in euchromatic islands (mRNA microarray)

city: Marseille

first: Christophe

last: Laloi

state: France

address: 163 avenue de Luminy

department: Biology

institute: Aix-Marseille Université

summary: The plant Topoisomerase VI complex has been implicated in a wide array of biological processes but little is known about its precise molecular role. In this study, we provide evidence that Topo VI acts as a chromatin barrier between chromatin territories by interacting with methionine adenosyltransferases (MAT), which produce the universal donor of methyl groups S-adenosyl-methionine (SAM). We first show that pericentromeric transposable elements (TEs) are awakened whereas  euchromatic island genes (EIGs) within heterochromatin are downregulated in mutants of the Topo VI complex. Consistent with this, the level of repressive H3K9me2 marks increases at EIGs loci while it decreases at TEs in a hypomorphic Topo VI mutant. We demonstrate that the Topo VI complex can interact with the SAM synthase MAT3 and drives it to TEs. A deficiency of Topo VI induces relocation of MAT3 from TEs to EIGs islands, leading to the levelling of the H3K9me2 mark and hence heterochromatin spreading.

overall_design: The transcriptome analysis of the caa39 mutant comprises three biological replicates for mutant and WT genotypes. The ChiPseq analysis of H3K9me2 includes a comparison of a pool of two biological replicates for caa39 and wt. This was done in duplicate for H3K27me3. In addition, an input chromatin control comprising a pool of two biological replicates was used for both genotypes. In total, we analyzed 6 RNAseq samples, and 6 ChIP samples and 2 input chromatin samples.

first: Louis-Valentin

last: Méteignier

first: Cécile

last: Lecampion

last: Vriet

first: Michel

last: Térèse

first: Martin

last: Rougée

first: Christian

last: Breuer

first: Ludivine

last: Soubigou-Taconnat

first: Keiko

last: Sugimoto

first: Frédy

last: Barneche


title: Gpnmb secreted from liver promotes lipogenesis in white adipose tissue and aggravates obesity and insulin resistance

city: Wuhan, Hubei Province

first: Song

last: Bao-Liang

address: College of Life Sciences

institute: Wuhan university

summary:
Metabolism in mammals is regulated by the complex interplay among different organs. Fatty acid synthesis is increased in white adipose tissue (WAT) when it is inhibited in liver. Here we identify glycoprotein nonmetastatic melanoma protein B (Gpnmb) as one liver-WAT cross-talk factor in lipogenesis. Hepatic SREBP pathway inhibition leads to increased transcription of the Gpnmb and promotes the processing of the membrane protein to a secreted form. Gpnmb stimulates lipogenesis in WAT and exacerbates diet-induced obesity and insulin resistance. In humans, Gpnmb is tightly associated with body mass index and is a strong risk factor for obesity. Gpnmb inhibition by a neutralizing antibody or liver specific knockdown improves metabolic parameters including weight gain reduction and increased insulin sensitivity, likely by promoting the beiging of WAT. These results suggest that Gpnmb is a liver-secreted factor regulating lipogenesis in WAT, and that Gpnmb inhibition may provide a therapeutic strategy for obesity and diabetes.
Hepatic SREBP pathway inhibition, such as liver-specific ablation of Scap (L-Scap-/-), decreases fatty acid synthesis in liver. Meanwhile, the fatty acid synthesis in white adipose tissue of L-Scap-/- is compensatorily increased. The microarray analysis using the liver RNAs of L-Scap-/- and wild type (WT) mice is performed to identify the up-regulated genes encoding secreted factors in L-Scap-/-.

overall_design: Total liver RNAs isolated from 8-week-old L-Scap-/- mice and WT littermates (n = 2 mice per group) subjected to microarray analysis

first: Bao-Liang

last: Song

first: Zhang-Sen

last: Zhou


title: Transcriptional response to diets varying in calcium and phosphorus levels in pigs

city: Dummerstorf

first: Klaus

last: Wimmers

address: Wilhelm-Stahl-Allee 2

department: Genome Biology

institute: FBN Dummerstorf

summary: in vivo microarray study of transcriptional changes in porcine peripheral blood mononuclear cells (PBMCs) due to variable dietary intake of calcium and phosphorus

overall_design:
per dietary group 6-7 pigs were collected for expression profiling
ANOVA

first: Petra

last: Wolf

first: Michael

last: Oster

last: Gerlinger


title: EZH2-mediated primary cilium deconstruction drives metastatic melanoma formation

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

summary: Human melanomas frequently harbor amplifications of EZH2. However, the oncogenic contribution of this methyltransferase to melanoma formation has remained elusive. Taking advantage of murine melanoma models, we now show that EZH2 drives tumorigenesis from benign BrafV600E or NrasQ61K-expressing melanocytes. EZH2 oncogenicity results from silencing of genes relevant for the integrity of the primary cilium, a signaling organelle projecting from the surface of vertebrate cells. Consequently, gain of EZH2 function promotes loss of primary cilia in benign melanocytic lesions. In contrast, blockade of EZH2 activity evokes ciliogenesis and cilia-dependent growth inhibition in malignant melanoma. Finally, we demonstrate that loss of cilia enhances pro-tumorigenic WNT/β-catenin signaling and is itself sufficient to drive metastatic melanoma in benign cells. Thus, primary cilia deconstruction is a key process in EZH2-driven melanomagenesis.

overall_design: RNA-seq of NrasQ61K versus NrasQ61K Ezh2Y646N dermal hyperplasia cells.

first: Daniel

last: Zingg

first: Lukas

last: Sommer


title: Engineering a haematopoietic stem cell niche by reprogramming mesenchymal stromal cells (RNA-Seq)

first: Fumio

last: Nakahara

overall_design: Examination of 4 different cell types; freshly sorted CD45(-) Ter119(-) CD31(-) Scf-GFP(-) cells, CD45(-) Ter119(-) CD31(-) Scf-GFP(+) cells, rMSCs and control vector-transduced stroma, n=3 for each cell type.

first: Paul

last: Frenette

first: Avi

last: Ma'ayan

first: Zichen

last: Wang


title: Histological Chorioamnionitis Induces Differential Gene Expression in Human Cord Blood Mononuclear Leukocytes from Term Neonates

city: Philadelphia

first: Zubair

middle: H

last: Aghai

state: PA

address: 833 Chestnut Street, Suite 1201

department: Pediatrics/ Neonatology

institute: Thomas Jefferson University/ Nemours

summary:
Human transcriptome array analysis of human cord blood mononuclear leokocytes from neonates exposed to histological chorioamnionitis and compared with healthy neonates
Histological chorioamnionitis (HCA) is an infection of fetal membranes and complicates 5.2% to 28.5% of all live births. Exposure to HCA may have long-term consequences including an increased risk for allergic disorders and asthma later in childhood, the mechanism(s) of which are still not yet well understood. Our objective was to determine the mRNA transcriptome of cord blood mononuclear leukocytes from term neonates and identify key genes and pathways involved in HCA. We found several key genes differentially expressed with exposure to HCA.  These transcriptomes included novel genes and pathways associated with exposure to HCA. The differential gene expression included the key genes regulating inflammatory, immune, respiratory and neurological pathways, which may contribute to disorders in those pathways in neonates exposed to HCA.

overall_design: We analyzed  gene expression from cord blood mononuclear leukocytes (5 histological chorioamnionitis exposed neonates and 5 healthy control neonates) using the Affymetrix Human transcriptome array 2.0. Array data was processed by Affymetrix Array Computational Tool.

first: Suhita

last: Gayen nee’ Betal

first: Swati

last: Murthy

last: Favara

first: Gina

last: Fong

first: Joanna

last: Chan

first: Sankar

last: Addya

first: Thomas

last: Shaffer

first: Jay

last: Greenspan

first: Vineet

last: Bhandari

first: Irfan

last: Rahman


title: In human sperm, H4K20me3 is abundantly preserved in retrotransposons, satellite repeats and olfactory genes, and maintains herewith the somatic-like pattern

city: Liège

first: Nor Eddine

last: Sounni

address: avenue de l'Hôpital 11

department: Medical oncology

country: Belgium

institute: Liège University (ULG - ULiège)

summary: In human sperm, preserved histones evading histone-to-protamine replacement were observed in certain genes and gene promoters, but also in distal intergenic and repetitive DNA regions. The substantiality of the latter and its putative biological role are still a subject of hot debate. To shed more light on this issue we analyzed H4K20me3, a histone mark regulating heterochromatic and repetitive DNA in somatic cells, which was recently detected in human sperm. Our immunohistochemical and western blot analyses revealed the presence of H4K20me3 in male germ cells at every stage of spermatogenesis and in mature sperms, respectively. By ChIP-sequencing of the motile sperm fractions from three biological replicates we found 4.56% of the sperm genome to be occupied by H4K20me3. By comparing the genome-wide binding sites of H4K20me3 in sperm cells and somatic cells (K562) we found correspondences in 77% of respective peaks. The majority of binding sites (70%) were detected in distal intergenic and intron regions. Intriguingly, H4K20me3 enrichments could be observed in both somatic and sperm cells within satellite repeats and retrotransposons, particularly in long interspersed nuclear repeats (LINEs) and retrotransposons containing long terminal repeats (LTR-retrotransposons). Broad cluster arrangements and strong enrichments in olfactory receptor genes were also characteristic for H4K20me3. This is the first time H4K20me3 is characterized at the genome-wide level in human sperm and compared to somatic cells. Our results reveal that H4K20me3 constitutes the majority of histones preserved in matured human sperm and maintains a somatic-like distribution pattern.

overall_design: H4K20me3 ChIPseq data on human male germ cells and somatic cells

first: Nihan

last: Ozturk

first: Sabrina

last: Gies

first: Damien

last: Calay

first: Catherine

last: Creppe

first: Jan

last: Hendrickx

first: Temuujin

last: Dansranjavin

first: Undraga

last: Schagdarsurengin


title: Transcriptome wide identification of retained introns upon depletion of the splicing factors WBP11 or SNW1

city: Baltimore

first: Andrew

last: Holland

state: MD

address: 725 N Wolfe St PCTB 704

institute: Johns Hopkins University School of Medicine

summary: We identified introns that are dependent on WBP11 or SNW1 for efficient splicing. WBP11 and SNW1 were depleted by RNAi and compared to a mock transfected population of cells. WBP11 was also depleted by auxin and compared to an untreated population of cells

overall_design: RNA-Seq analysis of mRNA purified from colorectal adenocarcinoma cell lines depleted of either WBP11 or SNW1 by RNAi or by auxin-induced depletion of AID-tagged WBP11 transgene in an endogenous WBP11 knockout background

first: E

last: Park

first: A


title: Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis

city: Cambridge

first: Sanja

last: Vickovic

address: 415 Main Street

institute: Broad Institute of MIT and Harvard

overall_design: 4 timepoints in SOD1-G93A model with WT control; 2 timepoints in ATG7 model


title: Xenograft SH-SY5Y tumors with inducible NOTCH3-IC expression.

first: Richard

last: Volckmann

summary: Expression analysis of xenograft tumors of ADRN cell line SH-SY5Y with doxycycline-inducible NOTCH3-IC was used to study transcriptional reprogramming to a MES state in vivo.

overall_design: Mice with SH-SY5Y-NOTCH3IC tumors were administered doxycycline for 7 or 14 days to analyze mRNA.

first: Johan

last: van Nes


title: IL-23 producing IL-10Rα-deficient gut macrophages elicit an IL-22-driven pro-inflammatory epithelial cell response [dataset 2]

city: REHOVOT

first: Steffen

last: Jung

address: Herzl

department: Immunology and Regenerative Biology

institute: The Weizmann Institute of Science

summary: we define critical cell-type-specific contributions to the induction and effector mechanism of macrophage-driven colitis, as manifested in mice harboring IL-10R deficiencies and human IBD pathologies

overall_design: Examination of RNA expression changes in colonic macrophages extracted from different transgenic mice

first: Jung

last: Steffen

first: Bernshtein

last: Biana

first: David

last: Eyal


title: Analysis of the pre-mRNA splicing in the wild type

city: BEIJING

first: zhiqiang

last: li

address: NO. 2 yuanmingyuan west road

department: Institute of plant protection

institute: Chinese academy of agricultural sciences

summary: Identification of the difference of the pre-mRNA in the wild type and mutant strain

overall_design: wild type (WT) and mutant strain were generated by deep sequencing

first: Z

last: Li

first: W

last: Liu


title: LOSS OF THE TUMOR SUPPRESSOR, TP53, ENHANCES THE ANDROGEN RECEPTOR MEDIATED ONCOGENIC TRANSFORMATION AND TUMOR DEVELOPMENT IN THE MOUSE PROSTATE

city: Los Angeles

first: Sungyong

last: You

address: 8700 Beverly Blvd

department: Surgery

institute: Cedars-Sinai Medical Center

summary: Androgen signaling is essential for prostate tumorigenesis. The tumor suppressor p53 has been implicated in prostate cancer progression. Recent genome analysis of human prostate cancers demonstrated that both AR gene amplification and TP53 deletion are frequently altered in advanced prostate cancer. However, the biological role of these dual genetic alterations in prostate tumorigenesis is largely unknown. In addition, there are no biologically relevant models that can be used to assess these genetic abnormalities in the prostate.  Here, we report a novel mouse model, in which elevated transgenic AR expression and Trp53 deletion occur simultaneously in mouse prostatic epithelium to mimic what happens in human prostate cancer cells.  These compound mice developed an earlier onset of high-grade prostatic intraepithelial neoplasia and accelerated prostate tumors. Histological analysis showed pathological lesions resembling prostatic sarcomatoid and basaloid carcinomas with massive squamous differentiation in the above compound mice. RNA-sequencing analyses showed a robust enrichment of the signature genes for human prostatic basal cell carcinomas in the above prostate tumors. The Master Regulator Analysis further identified SOX2 as a transcriptional regulator in prostatic basal cell tumors. Elevated expression of SOX2 and its downstream target genes were detected in prostatic tumors of the compound mice. Chromatin immunoprecipitation analyses implicate a co-regulatory role of AR and SOX2 in the expression of prostatic basal cell signature genes. These results demonstrate a novel mechanism underlying elevated AR expression and Trp53 deletion induced prostate cancer cell trans-differentiation, aggressiveness, and progression.

overall_design: In search of the molecular basis for the collaborative role of transgenic AR expression and Trp53 deletion in prostate tumorigenesis, we performed RNA-sequencing (RNA-seq) to examine the global transcriptome profiles in the tumor tissue of different genotype mice.

first: Yongfeng

last: He

first: Julie

last: Yang

first: Zijie

last: Sun

first: Junhee

last: Yoon


title: Genome-wide analysis of total, cytoplasmic and nuclear levels of mRNA upon infection of A549 cells with A/WSN/1933 at an MOI of 5 for 6h.

city: Dallas

first: Beatriz

last: Fontoura

address: 6000 Harryhines Blvd

department: Cell Biology

institute: UT Southwestern Medical Center

summary: RNA of total cell, or nuclear fraction, or cytoplasmic fraction was prepared using RNeasy Plus mini Kit. Purified RNA was quantified by Nanodrop (Thermo Fisher). The RNA samples were subjected to transcriptome analysis using Illumina Human BeadChip 22k according to manufacturer’s instructions.

overall_design: A549 Cells are infected with A/WSN/1933 at an MOI of 5 for 6h and total cell extracts and also cytoplasmic and nuclear fractions are collected and subjected to mRNA microarray quantification.

first: Liang

last: Zhang


title: Engineering a haematopoietic stem cell niche by reprogramming mesenchymal stromal cells

city: Bronx

first: Fumio

last: Nakahara

address: 1301 Morris Park Ave., Price Center Rm. 107

institute: Albert Einstein College of Medicine

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

overall_design: Refer to individual Series


title: Cognate T cell interactions affect the DC transcriptome [dataset 4]

summary: Our data suggest that peptide-presenting DC receive signals from synapse-forming antigen specific CD4+ or CD8+ T cells that alter the DC expression profile. To further test this notion, we hock immunized T cell-engrafted mice with NP harboring CpG and coated with OVA (OVA / CpG NP) or the control antigen BSA (BSA / CpG NP) and isolated NP+ DC for RNAseq.

overall_design: NP+ DC were isolated 20 hrs post sub-cutaneous immunization with (OVA/CpG) NP or (BSA/CpG) NP from popliteal and inguinal lymph nodes. (OVA / CpG) or (BSA/CpG) NP+ DC were single-cell sorted into 384w-plates, barcoded and MARS-sequenced.

first: Caterina

last: Curato

first: Diego

middle: A

last: Jaitin

first: Amir

last: Giladi

first: Eyal

last: David

first: Dena

last: Leshkowitz


title: IL-23 producing IL-10Rα-deficient gut macrophages elicit an IL-22-driven pro-inflammatory epithelial cell response [dataset 1]

first: Steffen

last: Jung

first: Jung

last: Steffen

first: Bernshtein

last: Biana

first: David

last: Eyal


title: Illumina sequencing analysis of LINC00998 knockdown and control in Huh7 cell line

first: Zhiyong

last: Liu

state: China

address: changhai road 168

institute: Changhai Hospital

summary: shRNA knockdown against LINC00998 in Huh7 cells followed by RNA-seq. LINC00998 is also known as SMIM30 or ENSG00000214194.

overall_design: To examine the differentially expressed genes in LINC00998 knockdown and control cell samples

first: Yanan

last: Pang

first: Shanrong


title: Defining DC response to cognate T cell interaction in the antigen-challenged lymph node [dataset 3]

summary: We designed an experimental set up to probe DC responses to cognate T cell encounter in antigen draining LN

overall_design: We immunized mice that had been engrafted with antigen-specific T cells (OT-I, OT-II), with nanoparticles (NP) entrapping antigen (OVA), adjuvants (CpG) and a fluorescent dye (6G rhodamine) to study the immediate DC response to T cell encounter using bulk and single cell RNA-seq profiling.

first: Louise

last: Chappell-Maor