title: Mechanical stretch induces hair regeneration through the alternative activation of macrophages

status: Public on Jan 30 2019

city: HsinChu

first: Chih-Hung

last: Chou

address: 1001 University Road

country: Taiwan

institute: National Chiao Tung University

summary: Tissues and cells in organism are continuously exposed to a complicated set of mechanical cues from the environment. Mechanical stimulations affect cell proliferation, differentiation, migration, and determine tissue homeostasis as well as repair. By using a specially designed skin-stretching device, we discover hair stem cells proliferate in response to stretch and hair regeneration occurs only when proper strain and duration were delivered. Counterbalance between WNT and BMP-2 followed by a two-step mechanism was identified through molecular and genetic analyses. Macrophages were first recruited by chemokines elicited by stretch and polarized to M2 phenotype. Growth factors such as HGF and IGF-1 released by M2 macrophages then activated hair stem cells and facilitate hair regeneration. Collectively, a hierarchical control from mechanics, chemical signals, cell behaviors, to tissue responses was revealed. This novel finding shed new light on regenerative medicine and disease control since one can manipulate cellular processes through simple mechanical stimulation.

overall_design: By using a specially designed skin-stretching device to discover the hair stem cells biological process and hair regeneration mechanism.

first: Szu-Ying

last: Chu

first: Hsien-Da

last: Huang

first: Meng-Hua

last: Yen

first: Hsiao-Chin

last: Hong

first: Po-Han

last: Chao

first: Yu-Hsuan

first: Po-Yu

last: Chen

first: Shi-Xin

last: Nian

first: Yu-Ru

first: Li-Ying

last: Liou

first: Yu-Chen

last: Liu

first: Hui-Mei

first: Feng-Mao

last: Lin

first: Yun-Ting

last: Chang

first: Chih-Chiang

first: Oscar

middle: K

last: Lee


title: Spatial clustering and common regulatory elements lead to TGF-β induced concerted gene expression

city: Beijing

first: ruoyan

last: Li

address: Yiheyuan street

country: China

institute: Peking University

type: Expression profiling by high throughput sequencing

summary: Cellular responses require temporally concerted transcriptional regulation of multiple genes. A single-input-module motif with one transcription factor regulating multiple target genes can generate the coordinated gene expression. In eukaryotic cells, the local environment of a gene characterized by histone modifications, DNA methylations, and the three-dimensional chromosome structure also regulates its transcriptional activity. To examine how the local environment and transcriptional factor regulation is coupled, we performed combined analysis of time-course RNA-seq data of TGF-β treated MCF10A cells and corresponding epigenome and Hi-C data. We discovered, genes co-regulated by a common transcription factor has tendency to be close both in the linear DNA sequence and spatially. Specifically, we identified local spatial organization of over a hundred of AP1-regulated genes, and competition between hetero- and homo-dimeric AP1 fine-tunes the complex structure leading to differential expression of downstream genes sharing similar local environment. We suggest this spatial organization as a general regulation principle.

overall_design: Gene expression profiling of MCF10A cells with 7 different duration of TGF-beta inducing as well as one control group without inducing, each time point with 3 biological replicates.

first: Fan

last: Bai

first: Jianhua

last: Xing


title: Rbpj expression in regulatory T cells is critical for restraining TH2 responses [female spleen Treg and Tconv RbpjKO expression]

status: Public on Jan 31 2019

city: Mainz

first: Michael

last: Delacher

state: Rhineland-Palatinate

address: Langenbeckstrasse 1

department: Institute for Immunology

country: Germany

institute: University Medical Center of the Johannes Gutenberg-University Mainz

summary: The transcriptional regulator Rbpj is involved in T-helper (TH) subset polarization, but its function in Treg cells remains unclear. Here we show that Treg-specific Rbpj deletion leads to splenomegaly and lymphadenopathy despite increased numbers of Treg cells with a polyclonal TCR repertoire. A specific defect of Rbpj-deficient Treg cells in controlling TH2 polarization and B cell responses was observed, leading to the spontaneous formation of germinal centers and a TH2-associated immunoglobulin class switch as well as T-cell polarization into TH2 effector cells. The observed phenotype was environment-dependent and could be induced by infection with parasitic nematodes. Rbpj-deficient Treg cells adopted open chromatin landscapes and gene expression profiles reminiscent of tissue-derived TH2-polarized Treg cells, with a prevailing footprint of transcription factor Gata-3. The over-expression of Ilt3 rendered Rbpj-deficient Treg cells incompatible to specifically restrain TH2 responses, finally leading to severe and fatal lymphoproliferative disease.

overall_design: We isolated spleen cells from Treg Rbpj-deficient animals and wildtype counterparts. Cells were stained with antibodies and cell populations sorted by FACS. Total RNA was isolated and measured with gene expression microarry.

first: Markus

last: Feuerer


title: Newly defined ABCB5+ dermal mesenchymal stem cells promote healing of chronic iron overload wounds via secretion of interleukin-1 receptor antagonist

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

institute: University of Ulm

summary: Here we report the beneficial effects of a newly identified dermal cell subpopulation expressing the ATP-binding cassette subfamily B member 5 (ABCB5) for the therapy of non-healing wounds. Local administration of dermal ABCB5+-derived MSCs attenuated macrophage-dominated inflammation and thereby accelerated healing of full-thickness excisional wounds in the iron overload mouse model mimicking the non-healing state of human venous leg ulcers. The observed beneficial effects were due to interleukin-1 receptor antagonist (IL-1RA) secreted by ABCB5+-derived MSCs, which dampened inflammation and shifted the prevalence of unrestrained pro-inflammatory M1 macrophages towards repair promoting anti-inflammatory M2 macrophages at the wound site. The beneficial anti-inflammatory effect of IL-1RA released from ABCB5+-derived MSCs on human wound macrophages was conserved in humanized NOD-scid IL2rγnull mice. In conclusion, human dermal ABCB5+ cells represent a novel, easy accessible and marker-enriched source of MSCs which holds substantial promise to successfully treat chronic non-healing wounds in humans.

overall_design: Identification gene expression profiles between low and high passage cells

first: Karin

last: Scharffetter-Kochanek


title: Rbpj expression in regulatory T cells is critical for restraining TH2 responses [spleen RbpjKO and RbpjWT RNA-seq]

summary: The transcriptional regulator Rbpj is involved in T-helper (TH) subset polarization, but its function in Treg cells remains unclear. Here we show that Treg-specific Rbpj deletion leads to splenomegaly and lymphadenopathy despite increased numbers of Treg cells with a polyclonal TCR repertoire. A specific defect of Rbpj-deficient Treg cells in controlling TH2 polarization and B cell responses is observed, leading to the spontaneous formation of germinal centers and a TH2-associated immunoglobulin class switch. The observed phenotype is environment-dependent and can be induced by infection with parasitic nematodes. Rbpj-deficient Treg cells adopt open chromatin landscapes and gene expression profiles reminiscent of tissue-derived TH2-polarized Treg cells, with a prevailing footprint of the transcription factor Gata-3. Taken together, our study suggest that Treg cells require Rbpj to specifically restrain TH2 responses, including their own excessive TH2-like differentiation potential.

overall_design: We isolated Treg cells from spleens of affected Treg Rbpj-deficient animals and wildtype counterparts. Total RNA was isolated and subjected to gene expression analysis using RNA sequencing


title: RNA immunoprecipitation and sequencing of aminoacyl-tRNA synthetase-specific genes

status: Public on Feb 05 2019

city: Daejeon

first: Jong Hwan

last: Kim

address: 125 Gwahak-ro, Yuseong-gu

department: Genome structure research center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: To gain insight into the specificity of target mRNAs, we enriched mRNAs bound to TRS by immunoprecipitation with anti-TRS antibody, then performed RNA immunoprecipitation and sequencing (RIP-seq) and compared the mRNAs with those enriched by immunoprecipitation with IgG, anti-AlaRS, anti-PRS and anti-IRS antibodies.

overall_design: Examination of ARS-specific mRNAs by RIP-seq experiments by using specific TRS, AlaRS, IRS, and PRS antibodies

first: Shinhye

last: Park

first: Jong

middle: H

last: kim

first: Eun-Young

first: Seon

middle: Y

first: Myung


title: Rbpj expression in regulatory T cells is critical for restraining TH2 responses [spleen Treg and Tconv RbpjWT expression]


title: Rbpj expression in regulatory T cells is critical for restraining TH2 responses [lymph nodes RbpjWT and diseased RbpjKO expression]

overall_design: We isolated lymph nodes from affected Treg Rbpj-deficient animals and wildtype counterparts. Total RNA was isolated and subjected to gene expression analysis using Illumina Bead Chip technology


title: Plasminogen activator inhibitor 1 (PAI1) promotes actin cytoskeleton reorganization and glycolytic metabolism in triple negative breast cancer

status: Public on Jan 29 2019

city: Ann Arbor

first: Yu-Chih

last: Chen

state: MI

address: 1301 Beal Ave.

country: USA

institute: University of Michigan

summary: We altered the expression of PAI1 in SUM159 breast cancer cell line and would like to see the effects

overall_design: We compared the wild-type (WT) and PAI1 transfected SUM159 breast cancer cell line

first: Gary

last: Luker


title: Expression data of OsSHMT Arabidopsis

city: New Delhi

first: Vandna

last: Rai

state: Delhi

address: Pusa campus

department: Genomics

country: India

institute: NRCPB

summary:
Plants were exposed to NaCl (150mM) stress for 24 hours
We did the whole genome expression profiling of OsSHMT overexpressed and wild type Arabidopsis

overall_design: 14-days-old whole seedlings were subjected to NaCl stress and whole seeedlings were used for expression study

first: Nagendra

last: Singh


title: Fusion of reprogramming factors alters trajectory of somatic lineage conversion

city: Seoul

first: Chanhyeok

address: 5, Hwarang-ro 14-gil

department: Brain Science Institute

institute: KIST (Korea Institute of Science and Technology)

summary: Simultaneous expression of Oct4, Klf4, Sox2, and cMyc induces pluripotency in somatic cells (iPSCs). Replacing Oct4 with the neuro-specific factor Brn4 leads to the transdifferentiation of fibroblasts into induced neural stem cells (iNSCs). However, Brn4 was recently found to induce a transient acquisition of pluripotency before establishing the neural fate. We employed genetic lineage tracing and found that induction of iNSCs with individual vectors leads to direct lineage conversion. In contrast, polycistronic expression produces a Brn4-Klf4 fusion protein that enables the induction of pluripotency. Our study demonstrates that a combination of pluripotency and tissue-specific factors allows for direct somatic cell transdifferentiation, bypassing the acquisition of a pluripotent state. This result has major implications for lineage conversion technologies, which hold potential for providing a safer alternative to iPSCs for clinical application both in vitro and in vivo.

overall_design: Here we perform RNA-Seq experiments in induced neural stem cells.

first: Sergiy

last: Velychko

first: Kyuree

last: Kang

first: Hans

middle: R

last: Schöler

first: Dong

middle: W

last: Han


title: Mapping the heterogeneity of histone modifications on hepatitis B virus-DNA using liver needle biopsies obtained from chronically infected patients

status: Public on Feb 07 2019

city: Emeryville

first: Tobias

last: Flecken

state: CA

address: 5300 Chiron Way

department: Infectious Diseases

institute: Novartis Institutes for Biomedical Research

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Covalently closed circular DNA (cccDNA) forms the basis for replication and persistence of hepatitis B virus (HBV) in the chronically infected liver. We have previously shown through the analysis of de novo HBV infected cell lines that viral transcription is subject to regulation by posttranslational modifications (PTMs) of histone proteins bound to cccDNA. We now report the successful adaptation of this ChIPseq approach for the analysis of fine-needle patient liver biopsy specimens to investigate the role of histone PTMs in chronically HBV-infected patients. Using 18 specimens from patients in different stages of chronic HBV infection our work shows that the profile of histone PTMs in chronic infection is more nuanced than observed in our previous work largely focused on acute infection in in vitro models. Specifically, we find that the majority of recovered HBV sequences are associated with the activating histone PTM H3K4me3, in line with our previous findings. We further find that the striking interpatient variability of its deposition in this patient cohort is linked to viral transcription and patient HBeAg status. Unexpectedly, we detect a significant localized deposition of the inhibitory histone PTM H3K9me3 on HBV-DNA in select patient biopsies which was not observed previously. Altogether, our results show that current in vitro models of HBV infection are unable to fully recapitulate the complex epigenetic landscape of chronic HBV infection observed in vivo and demonstrate that fine needle liver biopsy specimens can provide sufficient material to further investigate the interaction of viral and host proteins on HBV-DNA.

sample_organism:
Homo sapiens
Hepatitis B virus

platform_organism:
Homo sapiens
Hepatitis B virus

overall_design: 18 liver biopsy specimens were analyzed with input, H3K4me3, and H3K27me3-ChIP for all of them as well as H3 and H3K9me3 ChIPs for select biopsies, as indicated in sample descriptions. Additionally, in vitro infected primary human hepatocytes and cell lines with or without known integrated HBV-DNA (HepG2-hNTCP, HepG2-HBV, Hep3B, PLC/PRF/5) were included as controls. All ChIPseq results for H3, H3K4me3, H3K9me3 were obtained in duplicate with independently constructed libraries. Input and H3K27me3 sequencing results were replicated for 5 and 2 biopsies, respectively. All sequencing results from in vitro models were obtained in duplicate. An overview as well as the average HBV-derived readcounts normalized to 106 total reads are found in avgRPM.xlsx

first: Marie-Anne

last: Meier

first: Peter

last: Skewes-Cox

first: David

middle: T

last: Barkan

first: Markus

last: Heim

first: Stefan

middle: F

last: Wieland

first: Meghan

middle: M

last: Holdorf


title: Effect of Arg2 overexpression on murine liver gene expression profiles

status: Public on Feb 06 2019

city: St. Louis

first: Brian

middle: Jesse

last: DeBosch

state: MO

address: 660 S. Euclid Ave, Box 8208

department: Pediatrics and Cell Biology & Physiology

institute: Washington University School of Medicine

summary: We demonstrate the effects of Arg2 overexpression on murine liver gene expression by high-throughput RNA sequencing

overall_design: Examination of transcriptome in murine liver 5 weeks after infection with adeno-associated virus 8 (AAV8) encoding eGFP or ARG2.

first: Yiming

last: Zhang


title: Bcor loss perturbs myeloid differentiation and promotes leukaemogenesis [20wRNA-seq]

city: New York

first: Madison

last: Kelly

state: NY

address: 413 E69th Street

institute: Weill Cornell Medicine

summary: Investigation of the gene expression changes induced by Bcor loss in myeloid progenitors

overall_design: BcorΔE9-10 or relevant WT control mice were aged for 20 weeks, then myeloid progenitor cells were isolated and 3' RNA-sequencing was performed.

middle: J

first: Stephin

last: Vervoort


title: A Unique insight into the MiRNA profile during Genital Chlamydial Infection

status: Public on Jan 27 2019

city: Atlanta

first: Yusuf

last: Omosun

state: GA

address: 720 Westview Dr SW

department: Microbiology, Biochemistry and Immunology

institute: Morehouse School of Medicine

type: Non-coding RNA profiling by high throughput sequencing

summary:
Genital C. trachomatis (CT) infection may cause pelvic inflammatory disease (PID) that can lead to tubal factor infertility (TFI). Understanding the pathogenesis of chlamydial complications including the pathophysiological processes within the female host genital tract is of immense importance in preventing adverse pathology. In this study, we tested the hypothesis that the miRNA profile of a acute primary chlamydial infection characterized by temporary inflammation versus the profile associated with chronic genital chlamydial infections that might precipitate PID or TFI will be different. Thus, we analyzed and compared the differentially expressed miRNAs that regulate CT pathogenesis after a single genital infection and those involved in the development of PID and TFI after repeat infections. Mice (Mus musculus) were infected with Chlamydia muridarum once or twice with a month interval between infections, and then sacrificed and genital tract tissues were collected at 1, 2, 4, and 8 weeks after infection. miRNAs were differentially expressed in both first infection and the re-infection; however, the miRNA expression profile was different for both groups. Pathway analysis showed that, amongst other functions, the differentially regulated miRNA might be regulating several pathways involved in cellular and tissue development, disease conditions and toxicity.

Grant number: 1SC2HD086066-03
Funding source: Eunice Kennedy Shriver National Institute of Child Health & Human Development
Title: Discovering Novel Biomarkers Predictive of Tubal Infertility Caused by Chlamydia.
Principal investigator: Yusuf Omosun
Date: 05/01/2015-04/30/2019

overall_design: Two groups of mice (first infection and re-infection) were infected intravaginally with C. muridarum .Three replicate genital tract samples were collected at weeks 1,2,4 and 8 post infection. Genital tract samples were evaluated for infectivity, pathology(including infertility),mRNA sequencing and proteomics.

middle: O

first: Ifeyinwa

last: Benyeogor


title: Two distinct interstitial macrophage populations coexist across tissues in unique subtissular niches [lung interstitial]

status: Public on Jan 26 2019

city: Singapore

first: Florent

last: Ginhoux

address: 8A Biomedical Grove, Immunos Building, Level 3

country: Singapore

institute: Singapore Immunology Network (SIgN), A*STAR

summary: Macrophages are a heterogeneous cell population involved in tissue homeostasis, inflammation and in multiple pathologies. Although the major tissue-resident macrophage populations have been extensively studied, interstitial macrophages (IMs) residing within tissue parenchyma remain poorly defined. Here, we studied IMs from murine lung, fat, heart and dermis. We identified two independent IM subpopulations that are conserved across tissues: Lyve1loMHCIIhiCX3CR1hi (Lyve1loMHCIIhi) and Lyve1hiMHCIIloCX3CR1lo (Lyve1hiMHCIIlo) monocyte-derived IMs, with distinct gene expression profiles, phenotypes, functions, and localisation. Using a mouse model of inducible macrophage depletion (SLCO2B1-DTR), we found that the absence of Lyve1hiMHCIIlo IMs exacerbated experimental lung fibrosis. Thus, we demonstrate that two independent populations of IMs exist across tissues and exhibit conserved niche-dependent functional programming.

overall_design: Mouse Lung Interstitial Macrophages single cell mRNA profiles

first: Svetoslav

last: Chakarov

first: Hwee

last: Lim

first: Leonard

last: Tan

first: Sheau

last: See

first: Josephine

last: Lum

first: Xiaomeng

first: Shihui

last: Foo

first: Satoshi

last: Nakamizo

first: Duan

last: Kaibo

first: Wan

last: Kong

first: Rebecca

last: Gentek

first: Akhila

last: Balachander

first: Daniel

last: Carbajo

first: Camille

last: Bleriot

first: Benoit

last: Malleret

first: John

last: Tam

first: Sonia

last: Baig

first: Muhammad

last: Shabeer

first: Sue-Anne

middle: E

last: Toh

first: Andreas

last: Schlitzer

first: Anis

last: Larbi

first: Thomas

last: Marichal

first: Bernard

last: Malissen

first: Jinmiao

last: Chen

first: Michael

last: Poidinger

first: Kenji

last: Kabashima

first: Marc

last: Bajenoff

first: Lai

middle: G

last: Ng

first: Veronique

last: Angeli


title: RNAseq of unstimulated human neutrophil granulocytes.

status: Public on Feb 01 2019

city: Parkville

first: Sara-Jane

last: Dawson

state: VIC

address: 305 Grattan street

country: Australia

institute: Peter MacCallum Cancer Center

summary: Human neutrophils were isolated with negative selection (Miltenyi MacsXpress, purity > 99%) from fresh venous blood. RNA was isolated directly after without stimulating the cells.

overall_design: Neutrophil transcriptome in the unstimulated cell.

first: Piotr

last: Grabowski

first: Sebastian

last: Hesse

first: Christoph

last: Klein

first: Juri

last: Rappsilber


title: RNA-sequencing of human mammary epithelial cells (HMLEs) engineered to express either ER or ER-SOX4 with and without 4-OHT to induce nuclear translocation

city: Utrecht

first: Ana

last: Lourenço

address: Uppsalalaan 8

country: Netherlands

institute: UMC Utrecht

summary: Through RNA-sequencing we analysed the differentially expressed genes upon inducible activation of SOX4.

overall_design: RNA-sequencing of human mammary epithelial cells (HMLEs) that were lentivirally transduced with vectors that contain expression cassettes with either a tamoxifen-inducible partial EstrogenReceptor (ER) or a fusion between ER and SOX4 (ER-SOX4). Both lines were analyzed with and without activation by nuclear translocation with 4OH-tamoxifen.

first: S

last: Vervoort

first: A

first: P

last: Coffer


title: RNA microarray studies of aspirin's effect on MnSOD-deficient mutant [EG110, (MT)] and wild-type [EG103, (WT)] Saccharomyces cerevisiae yeast cells

city: Msida

first: Rena

last: Balzan

address: Tal-Qroqq

department: Physiology & Biochemistry

country: Malta

institute: University of Malta

summary: Non-steroidal anti-inflammatory drugs, principally aspirin (acetylsalicylic acid, ASA), have anti-neoplastic properties, as shown by epidemiological studies on colorectal cancer and many other types of tumours. The chemopreventive and anti-proliferative properties of aspirin towards tumour cells have been shown to be due to the induction of programmed cell death such as apoptosis. Yeast cells are among the experimental models used extensively for the study of oxidative stress and apoptosis in living organisms because yeast, such as S. cerevisiae, retains many of the core eukaryotic cellular processes, including the hallmarks of eukaryotic apoptosis.    An important contribution of our previous work has been the clarification of the critical defensive role of the antioxidant mitochondrial enzyme manganese superoxide dismutase (MnSOD) against apoptosis, confirmed to be the attenuation of aspirin-induced superoxide radical accumulation in the yeast mitochondria (Farrugia et al. (2013) FEMS Yeast Res 13, 755-768).    To study the possible differential expression of gene transcripts in relation to the induction of apoptosis by aspirin, we used gene expression profiling by means of GeneChip® Microarray Technology (Affymetrix®). The yeast strains considered for this study included (1) the wild type strain S. cerevisiae EG103, which contains both MnSOD and cytosolic copper, zinc superoxide dismutase (CuZnSOD) and (2) the redox-compromised MnSOD-deficient S. cerevisiae EG110 strain. [This work was financed by the Malta Council for Science and Technology through the R&I Technology Development Programme (Project R&I-2015-001)].

platform_organism:
Schizosaccharomyces pombe
Saccharomyces cerevisiae

overall_design: 1x108 yeast cells were harvested after 48 hours (h) of aerobic growth in ethanol medium (YPE) in the absence and presence of 15 mM ASA, at 28∘C with constant shaking at 250 rpm. The cells were mechanically lysed using a micro-minibeadbeater (Biospec), in the presence of acid-washed glass beads (500 micrometer diameter) and lysis buffer RLT provided with the Qiagen® RNeasy Mini Kit. Total yeast RNA was extracted and purified using the Qiagen® RNeasy Mini Kit including on-column DNase I digestion, according to the manufacturer’s instructions. The quantity and quality of total RNA were determined using a Thermo Scientific™ Nanodrop spectrophotometer and an Agilent™ 2100 Bioanalyser. A 500 ng quantity of total RNA from each biological replicate of cells, grown in both the absence or presence of aspirin, was analyzed by microarrays. The quality of the total RNA samples and the resulting complimentary RNA (cRNA) was assessed using the Bioanalyzer. Fragmented biotin-labeled cRNA was prepared and 7.5 micrograms was hybridized to GeneChip® Yeast Genome 2.0 Array Chips (Affymetrix®), according to the manufacturer’s protocols (Affymetrix®). The data was normalized using the Robust Multi-Array average (RMA) method, implemented AltAnalyze Version 2.0.8.1 (University of Cincinnati).

first: Gianluca

last: Farrugia


title: FoxP3 and Ezh2 Regulate Tfr cell Suppressive Function and Transcriptional Program

status: Public on Jan 25 2019

city: Boston

first: Peter

last: Sage

address: 221 Longwood Ave

department: Medicine/Renal

institute: Brigham and Women's Hospital

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

overall_design: Refer to individual Series


title: FoxP3 and Ezh2 Regulate Tfr cell Suppressive Function and Transcriptional Program [InVitro Ex-Tfr]

summary: InVitro Ex-Tfr RNAseq

overall_design: Examination of three cell types in Vitro


title: Rbpj expression in regulatory T cells is critical for restraining TH2 responses

first: Michael

last: Delacher

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

The transcriptional regulator Rbpj is involved in T-helper (TH) subset polarization, but its function in Treg cells remains unclear. Here we show that Treg-specific Rbpj deletion leads to splenomegaly and lymphadenopathy despite increased numbers of Treg cells with a polyclonal TCR repertoire. A specific defect of Rbpj-deficient Treg cells in controlling TH2 polarization and B cell responses is observed, leading to the spontaneous formation of germinal centers and a TH2-associated immunoglobulin class switch. The observed phenotype is environment-dependent and can be induced by infection with parasitic nematodes. Rbpj-deficient Treg cells adopt open chromatin landscapes and gene expression profiles reminiscent of tissue-derived TH2-polarized Treg cells, with a prevailing footprint of the transcription factor Gata-3. Taken together, our study suggest that Treg cells require Rbpj to specifically restrain TH2 responses, including their own excessive TH2-like differentiation potential.


title: Two distinct interstitial macrophage populations coexist across tissues in unique subtissular niches [FACs sorted]

first: Florent

last: Ginhoux

overall_design: FACS sorted cells from several animals

first: Svetoslav

last: Chakarov

first: Hwee

last: Lim

first: Leonard

last: Tan

first: Sheau

last: See

first: Josephine

last: Lum

first: Xiaomeng

last: Zhang

first: Shihui

last: Foo

first: Satoshi

last: Nakamizo

first: Duan

last: Kaibo

first: Wan

last: Kong

first: Rebecca

last: Gentek

first: Akhila

last: Balachander

first: Daniel

last: Carbajo

first: Camille

last: Bleriot

first: Benoit

last: Malleret

first: John

last: Tam

first: Sonia

last: Baig

first: Muhammad

last: Shabeer

first: Sue-Anne

last: Toh

first: Andreas

last: Schlitzer

first: Anis

last: Larbi

first: Thomas

last: Marichal

first: Bernard

last: Malissen

first: Jinmiao

last: Chen

last: Poidinger

first: Kenji


title: CNV  patterns in BRAFi resistant melanoma cell lines

city: Debrecen

first: Viktoria

last: Koroknai

address: 26/B Kassai str.

department: Department of Public Health and Epidemiology

country: Hungary

institute: University of Debrecen

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

summary: Genome variation profiling of BRAFi resistant melanoma cell lines comapered to the original ones by Affymetrix CytoScan 750K microarray

overall_design: BRAFi resistant melanoma cell line

first: Margit

last: Balázs


title: Clonal Analyses of Refractory Testicular Germ Cell Tumors

status: Public on Feb 26 2019

city: Scottsdale

first: Michael

middle: Thomas

last: Barrett

state: AZ

address: 13400 East Shea Boulevard

department: Molecular Pharmacology and Experimental Therapeutics

institute: Mayo Clinic Arizona

summary: We used DNA content-based flow cytometry to distinguish and isolate nuclei of clonal tumor populations from primary and metastatic refractory testicular germ cell tumors (TGCTs) tissues. We then interrogated each sorted tumor populationwith whole genome aCGH and next generation sequencing (NGS). we have explored the clonal basis of refractory TGCT by investigating distinct tumor populations that were present in each tumor. Notably this included resected primary tissues and treatment refractory metastases that arose after high dose chemotherapy. These results provide new knowledge regarding the role of clonal selection and selected genomic lesions in the resistance to chemotherapy in TGCT within this exceptional cohort.

overall_design: We applied a systematic approach combining DNA content flow cytometry, whole genome copy number and whole exome sequence analyses to interrogate tumor heterogeneity in primary and metastatic refractory testicular germ cell tumors (TGCTs). We identified both known and novel somatic copy number aberrations and mutations including candidate markers for platinum resistance that were present in a primary tumor of mixed histology and that remained after tandem autologous stem cell transplant..

first: Elizabeth

last: Lenkiewicz

first: Smriti

last: Malasi

first: Melissa

last: Stanton

first: James

last: Slack

first: Paul

last: Andrews

first: Lance

last: Pagliaro

first: Alan

last: Bryce


title: FoxP3 and Ezh2 Regulate Tfr cell Suppressive Function and Transcriptional Program [Ezh2]

first: Peter

last: Sage

summary: Tfr cells from Ezh2 floxed FoxP3 Cre mice

overall_design: Examination of Tfr cells with or without Ezh2 deletion


title: Dual inhibition of EZH1/2 depletes stem cells and over-activates WNT signaling in multiple myeloma [ChIP-seq]

city: Durham

first: Makoto

last: Nakagawa

state: NC

address: 308 Research Drive

department: Department of Orthopaedic Surgery

institute: Duke University

summary: Multiple myeloma (MM) is a hematological malignancy caused by accumulation of abnormal clonal plasma cells. Despite the recent development of novel therapies, relapse of MM eventually occurs due to a remaining population of drug-resistant myeloma stem cells. Side population (SP) cells exhibit cancer stem cell-like characteristics in MM; thus targeting these cells is a promising strategy to completely cure this malignancy. Here, we showed that SP cells expressed higher levels of enhancer of zeste (EZH) 1 and EZH2, which encode the catalytic subunits of Polycomb repressive complex 2 (PRC2), than non-SP cells, suggesting that EZH1/2 are both potential therapeutic targets to eradicate myeloma stem cells. A novel EZH1/2 dual inhibitor, OR-S1, effectively eradicated SP cells and had a greater antitumor effect than a selective EZH2 inhibitor in vitro and in vivo, including in a patient-derived xenograft model. Moreover, long-term continuous administration of OR-S1 completely cured mice bearing orthotopic xenografts. Additionally, PRC2 directly regulated WNT signaling, and over-activation of this signaling induced by dual inhibition of EZH1/2 eradicated myeloma stem cells. Our results demonstrate that dual inhibition of EZH1/2 is a promising therapeutic approach to eradicate myeloma stem cells, leading to significant advances in the treatment of MM.

overall_design: Histone modifications of two MM cell lines were examined by deep sequencing.

first: Issay

last: Kitabayashi


title: Dual inhibition of EZH1/2 depletes stem cells and over-activates WNT signaling in multiple myeloma [RNA-seq]

overall_design: Examination and comprison of transcriptomes of MM cells with or without OR-S1 treatment.


title: Transcriptomic analysis of frontal fibrosing alopecia

city: London

first: Venu

middle: Madhav

last: Pullabhatla

address: Great Maze Pond

department: Guy's Hospital

country: United Kingdom

institute: Biomedical Research Centre

summary: We undertook transcriptome profiling with RNA-sequencing of scalp skin from seven cases of European ancestry and seven matched controls.

overall_design: Transcriptomic analysis was undertaken in 7 cases vs 7 matched controls with the objective to identify significantly differentially expressed genes and perform pathway analysis thereof.

first: Christos

last: Tziotzios

first: John

last: McGrath


title: Effect of apicidin on gene expression in Staphylococcus aureus USA300 strain LAC

city: Aurora

first: Alexander

last: Horswill

state: CO

department: Immunology and Microbiology

institute: University of Colorado Anschutz Medical Campus

summary: The fungal metabolite apicidin acts as a quorum sensing inhibitor in Staphylococcus aureus. Here we use RNA-sequencing to examine the effect of apicidin on gene expression, comparing to untreated wild-type and an agr quorum sensing mutant.

sample_organism: Staphylococcus aureus subsp. aureus USA300

overall_design: Illumina RNA-sequencing of S. aureus USA300 LAC and LAC Δagr +/- 100 μM apicidin, in triplicate.

first: Corey

middle: P

last: Parlet

first: Jeffrey

middle: S

last: Kavanaugh

first: Heidi

middle: A

last: Crosby

first: Huzefa

last: Raja

first: Tamam

last: El-Elimat

first: Daniel

last: Todd

first: Cedric

last: Pearce

first: Nadja

middle: B

last: Cech

first: Nicholas

last: Oberlies


title: RNA sequencing of whole Dorsal Root Ganglia (DRG) and laser captured large diameter DRG neurons upon Environmental Enrichment (EE) compared to Standard Housing (SH)

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

summary:
Purpose: A) compare the gene expression in whole DRG and in large diameter DRG neurons of mice exposed to EE compared to SH

Results: we found that EE induces transcriptional changes promoting axon regeneration

overall_design: Method: RNA-seq from sciatic L4-L6 DRG extracted from mice housed for 10 days in EE vs SH. For whole DRG, pool of sciatic DRGs from 2 mice were used for each sample. DRG were collected in RNase later reagent, and crushed with RNase free micropestle for RNA extraction. For laser captured DRG, sciatic large diameter DRG were extracted from 3 mice for each sample. Using RNase-free conditions, DRGs were embedded with Tissue Freezing Medium (Triangle Biomedical Sciences, Inc) and frozen in dry ice-cold 2-methylbutane. 16 µm thick sections were cut on the cryostat and collected on Leica PEN-membrane slides (Leica). From each animal, 4-6 slides were obtained. Toluidine blue (Sigma) staining was used to identify the DRG neurons. Slides containing sections were dehydrated and stained with ethanol series, as follow: 3 times of 30 seconds in 70% ethanol, 60 seconds in 0.5% Toluidine blue dissolved in 70% ethanol, 2 times for 30 seconds each in 70% ethanol, 1 time for 30 seconds in 90% ethanol, 2 times for 30 seconds in 100% ethanol. Once air-dried the slides underwent laser capture using a Leica LMD 6000 microscope. From each animal, large diameter neurons with a diameter of ≥ 30 microns were obtained

first: Thomas

last: Hutson

first: Ilaria

last: Palmisano

first: Simone

last: Di Giovanni

first: Dejan

last: Lazarevic


title: Comparative analysis reveals a role for TGF-β in shaping the residency-related transcriptional signature in tissue-resident memory CD8+ T cells

status: Public on Jan 23 2019

city: Melbourne

first: Artika

middle: Praveeta

last: Nath

address: 75 commerical road

institute: Baker Heart and Diabetes Institute

summary: Tissue-resident CD8+ memory T (TRM) cells are immune cells that permanently reside at tissue sites where they play an important role in providing rapid protection against reinfection. They are not only phenotypically and functionally distinct from their circulating memory counterparts, but also exhibit a unique transcriptional profile. To date, the local tissue signals required for their development and long-term residency are not well understood. So far, the best-characterised tissue-derived signal is transforming growth factor-β (TGF-β), which has been shown to promote the development of these cells within tissues. In this study, we aimed to determine to what extent the transcriptional signatures of TRM cells from multiple tissues reflects TGF-β imprinting. We activated murine CD8+ T cells, stimulated them in vitro by TGF-β, and profiled their transcriptomes using RNA-seq. Upon comparison, we identified a TGF-β-induced signature of differentially expressed genes between TGF-β-stimulated and -unstimulated cells. Next, we linked this in vitro TGF-β-induced signature to a previously identified in vivo TRM-specific gene set and found considerable (>50%) overlap between the two gene sets, thus showing that a substantial part of the TRM signature can be attributed to TGF-β signalling. Finally, gene set enrichment analysis further revealed that the altered gene signature following TGF-β exposure reflected transcriptional signatures found in TRM cells from both epithelial and non-epithelial tissues. In summary, these findings show that TGF-β has a broad footprint in establishing the residency-specific transcriptional profile of TRM cells, which is detectable in TRM cells from diverse tissues. They further suggest that constitutive TGF-β signaling might be involved for their long-term persistence at tissue sites.

overall_design: RNA-sequencing was used to profile the transcriptome of murine CD8+ T cells stimulated in vitro by TGF-β

first: Asolina

last: Braun

first: Scott

last: Ritchie

first: Francis

middle: R

last: Carbone

first: Laura

last: Mackay

last: Gebhardt

first: Michael

last: Inouye


title: mrps-5 RNAi C. elegans expression profiling

status: Public on Feb 19 2019

city: Lausanne

first: Yasmine

last: Liu

address: Station 19 CH-1015 Lausanne

department: Laboratory of intergrative systems physiology

country: Switzerland

institute: EPFL

summary: Gene expression analysis of Caenorhabditis elegans treated with siRNA of mitochondrial ribosomal protein-5, mrps-5

overall_design: RNAi experiments: strain used was N2 (Bristol). Bacterial feeding RNAi experiments: clone used was mrps-5 (E02A10.1) derived from Vidal library; Control was empty vector RNAi bacteria HT115; Culture temperature: 20 ℃; RNAi treatment starts at the L4 stage of parental worms and woms samples for microarray were harvested at the young adult phase of progenies; 500 worms per biological replicates; 4 replicates per condition; The raw data files of the control in this experiment including N2_HT115_replicate 1, N2_HT115_replicate 2, N2_HT115_replicate 3, N2_HT115_replicate 4 are already avaliable at Gene Expression Omnibus with GSE106672 at the time of this submission.

first: Georges

last: Janssens

first: Rashmi

last: Kamble

first: Arwen

middle: W

last: Gao

first: Aldo

last: Jongejan

first: Michel

last: van Weeghel

first: Alyson

last: MacInnes

first: Riekelt

middle: H

last: Houtkooper


title: EIF1AX-A113 splice and RAS mutations cooperate to drive thyroid tumorigenesis through ATF4 and c-MYC

status: Public on Jan 28 2019

city: Zurich

first: Gunnar

last: Rätsch

state: -None-

address: Universitatstrasse 6

department: Institute for Machine Learning

institute: ETH Zürich

summary: Translation initiation in higher eukaryotes is orchestrated by the tight regulation of the cap binding and the 43S pre-initiation complexes (PIC). The PIC component eukaryotic initiation factor 1A (EIF1A), encoded on human chromosomes X and Y by EIF1AX and EIF1AY, respectively, is essential for recruitment of the ternary complex and for assembling the 43S PIC, which after recruitment onto capped mRNAs scans their 5’UTR and localizes the AUG to initiate translation. Recurrent EIF1AX mutations are found in several cancers, including ~1% of papillary thyroid cancers in a mutually exclusive manner with other drivers (BRAF, RAS, and oncogenic fusions). They are enriched in advanced thyroid cancers (11%) where they display a striking co-occurrence with RAS, which we show cooperate to induce tumorigenesis in mouse models and in isogenic cell lines. The C-terminal tail EIF1AX-A113splice mutation is the most prevalent in advanced thyroid cancer, and private to this disease. We found that EIF1AX-A113spl variants stabilize the PIC and induces ATF4 expression, a sensor of cellular stress, which is co-opted to suppress EIF-2α phosphorylation, thus enabling a general increase in protein synthetic rate. RAS stabilizes c-MYC, an effect augmented by EIF1AX-A113spl. ATF4 and c-MYC induce expression of aminoacid transporters, and enhance sensitivity of mTOR to aminoacid supply. These mutually reinforcing events generate therapeutic vulnerabilities to MEK, BRD4 and mTOR kinase inhibitors. The RNA-Seq and Ribosome Profiling samples provided here were used to support the claim of increased translational efficiency of ATF4.

overall_design: Comparison of Ribosome footprints in the context of EIF1AX-splice mutated (C643) and splice reverted isogenic cell line (C643-spl- rev), three replicates of ribosome-protected RNA sequencing and three replicates of RNA-seq were used. Additionally, 3 replicates of RNA-seq comparing KRAS G12R mutant CAL62 vs. CAL62-splice, an isogenic cell line generated with CRISPR-Cas9 mediated knock in of EIF1AX-splice mutation.

first: James

last: Fagin

first: Gnana

last: Krishnamoorthy

first: Natalie

last: Davidson


title: Transcriptomic profiling of peripheral blood NK cells of chronic HBV, HCV and HIV patients

city: Rotterdam

first: Andre

last: Boonstra

address: Dr. Molewaterplein 40

department: Dept. of Gastroenterology and Hepatology

institute: Erasmus MC

summary:
Background: NK cells during chronic viral infection have been well studied over the last decade. We performed an unbiased next-generation RNA-sequencing approach to identify commonalities or differences of the effect of HIV, HCV and HBV viremia on NK cell transcriptomes.
Methods: Using cell sorting, we obtained CD3-CD56+ NK cells from blood of 6 HIV, 11 HCV, and 32 HBV infected and untreated patients. Library preparation and sequencing were done using Illumina mRNA-Seq Sample Prep Kit and the HiSeq 2000, HiSeq2500 or NextSeq 500, and further analysis by an in-house analytic pipeline.
Results: In NK cells from HIV, HCV and HBV patients, transcriptome analysis identified 272, 53, and 56 differentially expressed genes, respectively (fold change >1.5, q-value 0.2). Interferon stimulated genes were induced in NK cells from HIV/HCV patients, but not during HBV infection. HIV viremia downregulated ribosome assembly genes in NK cells. In HBV, viral load and ALT variation had little effect on genes related to NK effector function.
Conclusion: We compare, for the first time, NK cell transcripts of viremic HIV, HCV and HBV patients. We clearly demonstrate distinctive NK cell gene signatures in 3 different populations, suggestive for a different degree of functional alterations of the NK cell compartment as compared to healthy individuals.

overall_design: We analyzed NK cell transcripts collected from the blood of well-characterized chronic HBV patients (n=32), chronic HCV patients (n=8), and HIV patients (n=6). Differential gene expression analysis, global module analysis, and unsupervised clustering analysis were performed by employing RNA-sequencing on blood NK cell transcriptomes.

first: Lauke

middle: L

last: Boeijen

first: Jun

last: Hou

first: Rik

last: de Groen

first: Annelies

last: Verbon

first: André


title: Two distinct interstitial macrophage populations coexist across tissues in unique subtissular niches

first: Florent

last: Ginhoux


title: Mitotic chromosome binding predicts transcription factor properties in interphase

first: David

middle: Michael

last: Suter

address: EPFL SV-IN Station 19

department: Institute of Bioengineering

institute: École polytechnique fédérale de Lausanne


title: A TRIM71 binding long noncoding RNA Trincr1 represses FGF/ERK signaling in embryonic stem cells

city: Beijing

first: Yangming

last: Wang

address: 5 Yiheyuan Road

department: Institute of Molecular Medicine

institute: Peking University

summary: Long noncoding RNAs (lncRNAs) have emerged as important components of gene regulatory network in embryonic stem cells (ESCs). However, the function and molecular mechanism of lncRNAs are still largely unknown. Here we identified Trincr1 (TRIM71 interacting long noncoding RNA 1) lncRNA that regulates the FGF/ERK signaling and self-renewal of ESCs. Trincr1 is exported by THOC complex to cytoplasm where it binds and represses TRIM71, leading to the downregulation of SHCBP1 protein. Knocking out Trincr1 led to the upregulation of phosphorylated ERK and ERK pathway target genes and the decrease of ESC self-renewal, while knocking down Trim71 completely rescued the defects of Trincr1 knockout. Furthermore, ectopic expression of Trincr1 repressed FGF/ERK signaling and the self-renewal of neural progenitor cells. Together, this study reveals novel regulators in FGF/ERK signaling pathway and highlights lncRNA as an important player in cell signaling network to coordinate cell fate specification.

overall_design: Examination of differential expressed genes between WT and Trincr1-ko mouse embryonic stem cells grown in 2iL and PD+LIF media by poly(A)+ RNA-Seq. Two biological replicates were completed for each groups.Identification of Trim71 binding RNA were investigated by RIP-seq. Empty cells were used as negative control. Two biological replicates were completed for each groups.

first: Ya-Pu

last: Li

first: Fei-Fei

last: Duan

first: Yu-Ting

last: Zhao

first: Kai-Li

last: Gu

first: Le-Qi

last: Liao

first: Huai-Bin

last: Su

first: Jing

last: Hao

first: Kun

last: Zhang

last: Yang


title: Interferon Regulatory Factor-8 (IRF8) Expression in Macrophages Governs an Anti-Metastatic Program in Breast Cancer

city: BUFFALO

first: Eduardo

last: Cortes

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

institute: ROSWELL PARK CANCER INSTITUTE

summary: High macrophage infiltration in cancer is associated with reduced survival in animal models and in patients. This reflects a shift in the macrophage response from a tumor-suppressive to tumor-supportive program governed by transcriptional events regulated by the inflammatory milieu.  Although several transcription factors are known to drive a pro-metastatic program, those that govern an anti-metastatic program are less understood.  Interferon regulatory factor-8 (IRF8) is integral for macrophage responses against infections. Using a genetic loss-of-function approach, we tested the hypothesis that IRF8 expression in macrophages governs their capacity to inhibit metastasis. We found that:  1) metastasis was significantly increased in mice with IRF8-deficient macrophages; 2) IRF8-deficient macrophages displayed a neutrophil-like program enriched for metastasis-associated genes; and 3) lower IRF8 expression correlated with reduced survival in human breast cancer and melanoma with high or low macrophage infiltration. These data demonstrate a previously unrecognized role for IRF8 in macrophage biology to control metastasis.

overall_design: Bone marrow-derived macrophages were treated with IFN-ᵧ (100u/mL) or IL-4 (20ng/mL) for 24h, RNA isolated and RNA-Seq performed on the samples.

first: Danielle

middle: F

last: Twum

first: Sean

last: Colligan

first: Nicholas

last: Hoffend

first: Eriko

last: Katsuta

last: Cortes Gomez

first: Mary

last: Hensen

first: Mukund

last: Seshadri

first: Michael

middle: J

last: Nemeth

first: Scott

middle: I

last: Abrams


title: Low pH controls MondoA genome-wide binding.

city: Salt Lake City

first: Donald

last: Ayer

state: Utah

address: 2000 Circle of Hope

department: Oncological Sciences

institute: University of Utah

summary: Human MondoA requires glucose as well as other modulatory signals to function in transcription. One such signal is acidosis, which increases MondoA activity and also drives a protective gene signature breast cancer. How low pH controls MondoA transcriptional activity is unknown. We found that low pH medium increases mitochondrial ATP (mtATP), which is subsequently exported from the mitochondrial matrix. Mitochondria-bound hexokinase transfers a phosphate from mtATP to cytoplasmic glucose to generate glucose-6-phosphate (G6P), which is an established MondoA activator. The outer mitochondrial membrane localization of MondoA suggests that it is positioned to coordinate the adaptive transcriptional response to a cell’s most abundant energy sources, cytoplasmic glucose and mtATP. In response to acidosis, MondoA shows preferential binding to just two targets, TXNIP and its paralog ARRDC4. Because these transcriptional targets are suppressors of glucose uptake we propose that MondoA is critical for restoring metabolic homeostasis in response to high energy charge.

overall_design: HeLa cells were treated with either DMEM with normal pH or acidic DMEM for 4 hours.

first: Tian-Yeh

last: Lim


title: microRNA Expression data from Lung cancer cell lines

city: Hwasun-gun

first: Seung-won

last: Lee

state: Jeollanam-do

address: 264 Seoyang-ro, Hwasun-eup

institute: Chonnam National University Medical School

summary:
GPX3 has been reported to be involved in antioxidant, anticancer, and anti-inflammation in various studies. It is also known that expression of GPX3 is low in lung cancer tissues.
We performed a microarray using three lung cancer cell lines including A549, H1650, and H1975 lung cancer cell lines. Among these, A549 is highly expressed in GPX3 as compared with H1650 and h1975. Microarrays were used to analyze microRNAs showing other expression between A549 and the other two cell lines.

overall_design: Lung cancer cell lines (A549, H1650 and H1975) were microarrayed once each time.


title: X-Ray induced DNA-Hydroxymethylation changes

city: Munich

first: Benjamin

last: Becker

address: Neuherbergstr. 11

department: Genomics II

institute: Bundeswehr Institute for Radiobiology

type: Methylation profiling by high throughput sequencing

summary: In this study we addressed the question whether changes of DNA hydroxymethylation after X-ray irradiation occur in a random fashion or if they show preferences for specific regions or features. We did not only focus on gene loci and promotor sights but also on gene body hydroxymethylation alterations and associated changes in gene expression. A more profound insight into hydroxymethylation characteristics triggered by radiation could provide clues to mechanisms and consequences of cellular response to irradiation including the immediate consequence of DNA strand breaks associated with active DNA demethylation as well as the long term risk of tumorigenesis or other associated diseases.

overall_design: Analysis of DNA-hydroxymethylation changes after X-ray irradiation of IMR90 cell line 1 to 120 h after exposure and evaluation of associated gene expression changes.

first: Reinhard

last: Ullmann

middle: V


title: LSD1 pharmacological inhibition in SET-2 containing wild type and mutant LSD1

city: Cambridge

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

institute: Harvard University

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

overall_design: Refer to individual Series


title: FoxP3 and Ezh2 Regulate Tfr cell Suppressive Function and Transcriptional Program [tissue]

city: Boston

first: Peter

last: Sage

address: 221 Longwood Ave

institute: Brigham and Women's Hospital

summary: Tissue Specific Transcriptional Profiling of Tfh, Tfr, Treg and Tcon

overall_design: Examination of 4 cell types from 3 tissues


title: The effects of SOX4 on the global epigenetic landscape in Mammary Epithelial Cells

city: Utrecht

first: Ana

last: Lourenço

address: Uppsalalaan 8

institute: UMC Utrecht

summary: By chromatine-immunoprecipitating (ChIP) using the mammary epithelial cell line HMLE with a Doxycyclin-inducible overexpression of SOX4 we determined various histone modifications and presence of the POL2 polymerase in presence and absence of overexpressed SOX4.

overall_design: ChIP with antibodies against trimethylated H3K4, acetylated H3K27, methylated H3K27 and Pol2 was performed in the ER-SOX4 HMLE cell line with and without doxycycline

first: S

last: Vervoort

first: A

first: P

last: Coffer


title: circRNA/miRNA/mRNA sequence data of BPA exposed GC-2 cells and normally cultured cells.

status: Public on Jan 24 2019

city: Wuhan

first: Huimin

last: Li

address: 13th Hangkong Road

institute: Huazhong University of Science and Technology

summary:
Purpose: To profile the circular RNAs (circRNAs), microRNAs (miRNA), and mRNAs expression in BPA exposed GC-2 cells and normally cultured cells.
Methods: For circRNA sequencing, total RNA was depleted of rRNA and then linear RNAs by RNase R digestion. cDNA library was constructed according to the Illumina TruSeq library preparation protocol. The Hiseq3000 sequencing platform (Illumina, San Diego, CA, USA) was used for circRNA sequencing. The sequence depth is 10G. Sequences were mapped using STAR software against GRCm38/mm10 mouse reference genome in UCSC Known Genes databases. CIRCexplorer software was applied to analyze the back-spliced junction for circular RNA prediction.  Small RNA sequencing was performed on Hiseq2500in 10M sequence depth after regular small RNA library preparation. After adaptor trimming by FASTXToolkit (0.0.14), reads were aligned to the mouse genome (GRCm38/mm10) with Bowtie software (version 1.1.0). miRBase v21 and miRDeep2 were used to annotate or forecast new miRNAs respectively.Hiseq2500 platform was used to sequence mRNA in 6G depth after strand-specific library construction with TruSeq RNA LTPrep Kit (Illumina, San Diego, CA, USA). Clean reads were aligned to reference genome (mouse GRCm38/mm10) with STAR software. And StringTie and Cuffcompare were used for transcription assembly and novel transcription prediction.
Results: A total of 4706 and 6486 circRNAs were identified in normally grow GC-2 cells and BPA treated cells respectively, with most not reported in circBase. According to the screening criterion of two folds, 4821 circRNAs were up-regulated and 2855 circRNAs were down-regulated compared to control group. The amounts and kinds of circRNAs were generally enhanced under BPA stress. Similar to circRNAs, miRNA sequencing also showed that more miRNAs were up-regulated than down-regulated under BPA stress (689 up and 98 down by ≥2 folds). In mRNA sequencing, 2978 genes were up-regulated and 2381 were down-regulated by at least 2 folds after BPA treatment.
Conclusions: Our study was the first to delineate the full landscape of circRNAs/miRNAs/mRNAs in BPA induced reproductive toxicity. Many functional circRNAs and miRNAs were found to be activated under BPA exposure. They hold great promise to be developed as sensitive biomarkers for BPA exposure and targets for BPA toxity blocking.

overall_design: The mouse spermatocyte derived cell line GC-2 was exposed to 0 μM and 120μM BPA for 48 hours. Cells were harvested by Trizol and subject to convention RNA extraction procedures. And RNAs from the same sample were shared to three aliquots for the subsequent circRNA, miRNA and mRNA high-throughput sequencing.

first: Hui-Min

first: Hong-Gang


title: RNASeq of trigeminal ganglia of chicken and wild duck species

city: New Haven

first: Viktor

last: Feketa

state: CT

address: 333 Cedar St SHM BE58

department: Cellular & Molecular Physiology

institute: Yale University

summary: A major challenge in biology is to link cellular and molecular variations with behavioral phenotypes. Here, we approached this by studying somatosensory neurons from a panel of bird species from the family Anatidae, known for their tactile-based foraging behavior. We found that tactile specialists exhibit a proportional expansion of neuronal mechanoreceptors in trigeminal ganglia. The expansion of mechanoreceptors occurs via neurons with intermediately and slowly inactivating mechano-current. Such neurons contain the Piezo2 ion channel, whose expression positively correlates with the expression of factors responsible for the development and function of touch receptors. Conversely, Piezo2 expression negatively correlates with expression of molecules mediating the detection of temperature and pain, suggesting that the expansion of Piezo2-containing mechanoreceptors with prolonged mechano-current occurs at the expense of other types of sensory neurons. Our study reveals a general mechanism of tactile specialization in vertebrates at the level of somatosensory system.

sample_organism:
Aix sponsa
Anas platyrhynchos
Oxyura jamaicensis
Gallus gallus
Histrionicus histrionicus
Anas rubripes
Aythya affinis

overall_design: High-throughput deep sequencing of the mRNA isolated from trigeminal ganglia of 7 bird species; 3 biological replicates per species; Total of 21 samples.

first: Eve

last: Schneider

first: Evan

middle: O

last: Anderson

first: Marco

last: Mastrotto

first: Yury

last: Nikolaev

first: Elena

last: Gracheva

first: Sviatoslav

middle: N

last: Bagriantsev


title: Genome-wide binding of EHMT2 in RH41 ARMS cells.

city: Singapore

first: Reshma

last: Taneja

state: Singapore

address: 2 Medical Drive, MD9, National University of Singapore

department: Department of Physiology

institute: National University of Singapore

summary: We report the genome wide occupancy of G9a in RH41 Alveolar Rhabdomyosarcoma cell line.

overall_design: Examination of G9a peaks in RH41 cells.

first: R


title: LSD1 pharmacological inhibition in SET-2 containing wild type and mutant LSD1 [RNA-Seq]

first: Brian

summary: We characterized the effect of GSK-LSD1 treatment on gene expression for both wt SET-2 and drug-resistant SET-2 LSD1 (Leu659_Asn660insArg)

overall_design: For RNA-seq preparation, SET-2 cells were treated in triplicated with either DMSO (0.1% v/v) or 250 nM GSK-LSD1 for 48 after which RNA was harvested and prepared for RNA sequencing to assess transcriptional changes

first: Allison

middle: P

last: Siegenfeld


title: Differences in tissue immune cell populations following hematopoietic stem cell transplantation in Crohn’s disease patients

city: Barcelona

first: Azucena

last: Salas

address: Rosselló, 149-153

department: Gastroenterology

country: Spain

institute: IDIBAPS

summary: Treatment of severely refractory Crohn’s disease (CD) patients remains a clinical challenge. Recent studies show the efficacy of autologous hematopoietic stem cell transplant (HSCT) in these severely compromised patients. HSCT is thought to eliminate auto-reactive cells; however, no specific studies of immune reconstitution in CD patients are available. We studied a group of CD patients receiving autologous HSCT, with 50% of them achieving endoscopic drug-free remission. To elucidate the mechanism driving efficacy, we studied changes in the immune cell composition in tissue induced by HSCT.

overall_design: Biopsy mRNA profiles of 14 CD patients undergoing HSCT were generated by deep sequencing, using HiSeq-4000 platform (Illumina, San Diego, CA).

first: Ana

middle: M

last: Corraliza


title: Bach2 is a critical negative regulator of Tfh cell differentiation

city: Birmingham

first: Hui

last: Hu

state: ALABAMA

address: 845 19th Street South,BBRB Rm859

department: Microbiology

institute: University of Alabama at Birmingham

summary: T follicular helper (Tfh) cells are essential for germinal center B cell responses; however, the molecular mechanism underlying Tfh cell programming, in particular, the initial Tfh cell development, remains largely unknown. Here, we show that in vivo, despite enhanced non-Tfh effector functions, the deletion of transcription factor Bach2 still results in preferential Tfh cell differentiation. Mechanistically, the deletion of Bach2 leads to the induction of CXCR5 expression even before the up-regulation of Ascl2. Subsequently we identified a novel regulatory element in the murine CXCR5 locus that negatively regulates CXCR5 promoter activities in a Bach2-dependent manner. Furthermore, we find that Bach2 is also essential for CD4+ T cell memory including Tfh cell memory. These results demonstrate that Bach2 is a novel critical player in controlling Tfh cell responses.

overall_design: Transcriptome analysis of naive OT-II Bach2-WT and OT-II Bach2-conditional knockout (cKO), and ex vivo OT-II Bach2-WT and Bach2-cKO donor cells 3 days after immunization.

first: Jianlin

last: Geng


title: Time course of TGFbeta induced epithelial mesenchymal transition (EMT) in H358 NSCLC cells.

city: Stony Brook

first: John

middle: D

last: Haley

address: BST 9-168, SB Medical

institute: Stony Brook University

summary: The capacity of cancer cells to undergo epithelial mesenchymal trans-differentiation has been implicated as a factor driving metastasis, through the acquisition of enhanced migratory/invasive cell programs and the engagement of anti-apoptotic mechanisms promoting drug and radiation resistance. Our aim was to define molecular signaling changes associated with mesenchymal trans-differentiation in two KRas mutant NSCLC models. We focused on central transcription and epigenetic regulators predicted to be important for mesenchymal cell survival.

overall_design: RNA was harvested 0, 1, 2, 4, 6, 8, 18, 24, 72, 168, ~500 and ~4500 hours after TGFbeta addition and subjected to 50bp paired-end Illumina RNAseq analysis. Haley, J.A., Haughney, E., Ullman, E., Bean, J., Haley, J.D.* and Fink, M.Y. (2014) ‘Altered Transcriptional Control Networks with Trans-Differentiation of Isogenic Mutant KRas NSCLC Models’ Front. Oncology, doi/10.3389/fonc.2014.00344.

first: J

first: S

last: Thomson


title: mRNA profiling of human Multipotent Adipose-Derived Stem (hMADS) cells transfected with miR-29a and subjected to adipocyte differentiation

city: Vienna

first: Michael

last: Karbiener

address: Benatzkygasse 2-6 / G

department: Global Pathogen Safety

country: Austria

institute: Takeda

summary: The human microRNA hsa-miR-29a is a member of the miR-29 family of microRNAs, which is expressed in the adipogenic lineage. To identify putative direct target mRNAs of the miR-29 family, and to get an idea about potential functions of the miR-29 family in adipocyte development, we transfected human Multipotent Adipose-Derived Stem (hMADS) cells with miR-29a mimics (leading to elevation of intracellular levels of mature miR-29a). Subsequently, gene expression profiling was performed for hMADS cells at day 0 (48 h after transfection) and at day 3, i.e. 3 days after adipocyte differentiation was induced by a chemically defined medium.

overall_design: Two-condition experiment, hMADS cells transfected either with miR-29a mimics or a control (non-targeting) miRNA mimic (miR-C). Separate analysis of two distinct time points after transfection: day 0 (i.e. 48 h after transfection; 4 biological replicates); day 3 after induction of adipocyte differentiation (3 biological replicates). Biological replicates were indepently grown, transfected and harvested. On each array, one biological replicate of miR-29a-transfected cells was directly compared to the corresponding miR-C-transfected cells (serving as reference sample). All hybridizations were repeated with reversed dye assignment (dye-swap) as technical replicates.

first: Marcel

last: Scheideler


title: Promoterless extrachromosomal circular DNA, microDNA, autonomously produce short regulatory RNAs that suppress gene expression

city: Charlottesville,

first: Anindya

last: Dutta

email: ad8q@virginia.edu, pk7z@virginia.edu

state: VA

address: Room no. 1232, Jordan Hall

department: MD-BIOC BC/Mole Genetics~School of medicine

institute: University of Virginia

summary: Interest in extrachromosomal circular DNA (eccDNA) molecules has increased recently because of their widespread presence in normal cells across every species ranging from yeast to humans, their increased levels in cancer cells, and their overlap with oncogenic and drug-resistant genes. However, the majority of eccDNA are too small to carry protein coding genes and their function has remained unknown. We have tested functional capabilities of small eccDNA molecules, termed microDNA, by creating artificial microDNA molecules mimicking known microDNA sequences and have discovered that microDNA express functional small regulatory RNA including microRNA and novel si-like RNA. MicroDNA is transcribed in vitro and in vivo independent of a promoter sequence. MicroDNA which carry miRNA genes form transcripts which are processed into mature miRNA molecules, through the endogenous RNA-interference pathway, which repress a luciferase reporter gene as well as endogenous mRNA targets of the miRNA. Further, microDNA containing sequences of exons repress the endogenous gene from which the microDNA was derived through the formation of novel si-like RNA. We also show that endogenous microDNA associate with RNA polymerases subunits POLR2H and POLR3F. Together, these results suggest that microDNA actively modulate gene expression through the production of both known and novel regulatory small RNA.

overall_design: Circular DNA associate with RNA polymerases subunits POLR2H and POLR3F.

first: Pankaj

last: Kumar


title: Lineage-specific reorganization of nuclear peripheral heterochromatin and H3K9me2 domains

city: Philadelphia

first: Kelvin

last: See

state: PA

address: 3400 Civic Center Blvd, Smilow Center for Translational Research

department: Medicine

institute: University of Pennsylvania

summary: Dynamic and regulated organization of chromatin within the 3-dimensional space of the nucleus has been postulated to contribute to gene accessibility, gene expression, and cell fate. Here we define the genome-wide lineage-specific reorganization of nuclear peripheral heterochromatin as a multipotent P19 embryocarcinoma cell adopts either a neural or a cardiac fate. We demonstrate that H3K9me2 marked nuclear peripheral heterochromatin undergoes lineage-specific local reorganization during cell fate determination. Lineage-specific loss of H3K9me2 is associated with spatial repositioning of genomic loci away from the nuclear periphery as shown by high-resolution 3D immuno-fluorescence in situ hybridization (3D immuno-FISH). The lineage-specific repositioning of loci away from the nuclear periphery is not always associated with activation of gene expression, but a subset of these genes is transcriptionally activated. Master regulator Mef2c is specifically repositioned from nuclear periphery during early neurogenic differentiation, but not early cardiogenic differentiation, with associated transcript upregulation. Master regulator Myocd is specifically repositioned during early cardiogenic differentiation, but not early neurogenic differentiation, and is transcriptionally upregulated at later stages of cardiac differentiation. These results provide experimental evidence for lineage-specific regulation of nuclear architecture when the same multipotent progenitor cell adopts distinct fates.

overall_design: In this study, we examined the genome wide distribution of nuclear peripheral heterochromatin and global transcriptomic changes in multipotent undifferentiated P19 cells, Day 3 RA-treated and Day 3 DMSO-treated P19 cells. We performed H3K9me2 ChIP-seq to mark nuclear peripheral heterochromatin and H3 ChIP-seq as parallel control with three biological replicates per condition. We performed RNA-seq at day 3 and day 6 of differentiation with three biological replicates per condition to assess transcriptomic changes.

first: Yemin

last: Lan

first: Joshua

last: Rhoades

first: Rajan

last: Jain

first: Cheryl

last: Smith

first: Jonathan

middle: A

last: Epstein


title: Replication timing and epigenome remodelling are associated with the nature of chromosomal rearrangements in cancer [Bisulfite-Seq]

city: Darlinghurst

first: Qian

last: Du

state: NSW

address: 384 Victoria St

institute: Garvan Institute of Medical Research

summary: DNA replication timing is known to facilitate the establishment of the epigenome, however, the intimate connection between replication timing and changes to the genome and epigenome in cancer remain largely uncharacterised. Here, we perform Repli-Seq and integrated epigenome analyses and demonstrate that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing. A subset of altered replication timing domains are conserved across cancers from different tissue origins. Notably, late-replicating regions in cancer cells display a loss of DNA methylation, and a switch in heterochromatin features from H3K9me3-marked constitutive to H3K27me3-marked facultative heterochromatin. Finally, analysis of 214 prostate and 35 breast cancer genomes reveal that late-replicating regions are prone to cis and early-replication to trans chromosomal rearrangements. Together, our data suggests that the nature of chromosomal rearrangement in cancer is related to the spatial and temporal positioning and altered epigenetic states of early-replicating compared to late-replicating loci.

overall_design: Whole genome bisulphite sequencing was conducted in the MCF7 human breast cancer cell line.

first: Susan

last: Clark


title: Enhancer Domains in Gastrointestinal Stromal Tumor Regulate KIT Expression and are Targetable by BET Bromodomain Inhibition [ChIP-seq]

city: Worcester

first: Matthew

last: Hemming

address: 364 Plantation Street

institute: UMass Medical School

summary: Gastrointestinal stromal tumor (GIST) is a mesenchymal neoplasm characterized by activating mutations in the related receptor tyrosine kinases KIT or PDGFRA. GIST relies on expression of these unamplified receptor tyrosine kinase (RTK) genes through a large enhancer domain, producing high expression levels of the oncogene required for tumor growth. Though kinase inhibition is an effective therapy for many GIST patients, disease progression from kinase resistance mutations is common, and no other efficacious classes of systemic therapy exist. Given GIST’s reliance upon enhancer-driven expression of an RTK, we hypothesized that the enhancer domain could be therapeutically targeted by a BET bromodomain inhibitor (BBI). Treatment of GIST cells with BBIs led to cell cycle arrest, apoptosis and cell death, with unique sensitivity in GIST cells arising from attenuation of the KIT enhancer domain and reduced KIT gene expression. BBI treatment in KIT-dependent GIST cells produced genome-wide changes in the H3K27ac enhancer landscape and gene expression program, which was also seen with direct KIT inhibition using a tyrosine kinase inhibitor (TKI). Combination treatment with BBI and TKI led to synergistic cytotoxic effects in vitro and in vivo, with BBIs preventing tumor growth in TKI-resistant xenografts. A novel mechanism of resistance to select BBIs was found in GIST attributable to drug efflux pumps. These results define a therapeutic vulnerability and clinical strategy for targeting oncogenic kinase dependency in GIST.

overall_design: ChIP-seq from GIST cell lines treated with drug or DMSO control.

first: Hemming

last: Matthew


title: LSD1 pharmacological inhibition in SET-2 containing wild type and mutant LSD1 [ChIP-Seq]

first: Brian

last: Liau

summary: We characterized the changes in histone modifications as well as the localization of LSD1 and GFI1B for both wt SET-2 and drug-resistant SET-2 LSD1 (Leu659_Asn660insArg) treated with GSK-LSD1

overall_design: ChIP-seq for histone modifications as well as LSD1 and GFI1B in wt SET-2 and drug-resistant SET-2 LSD1 (Leu659_Asn660insArg) upon treatment with DMSO or GSK-LSD1

first: Allison

last: Siegenfeld

middle: B


title: RNA-sequencing analysis of murine Hematopoietic Stem Cells treated with Nicotinamide Riboside

status: Public on Jan 17 2019

city: Lausanne

first: Olaia

last: Naveiras

address: Route cantonale

institute: EPFL

summary: LT-HSC and ST-HSCs were FACS sorted (>10^4cells per sample), cultured for two days in presence or absence of 1 mM NR and total RNA extracted

overall_design: LT-HSCs (Lin-ckit+sca1+CD150+CD48-CD34-) and ST-HSCs (Lin-ckit+sca1+CD150+CD48-CD34+) were FACS-sorted and cultured for 2 days. Cultures were maintained in Stemline II (Sigma) supplemented with 100ng/ml SCF (R&D) and 2ng/ml Flt3 (R&D), +/ - 1 mM NR. NR was replenished after 24h into the culture media. At the end of the culture period, total RNAs were extracted using the Quick-RNA Microprep Kit (R1050, Zymo Reseach) following the manufacturer’s instructions.

first: Vasco

last: Campos

first: Pernille

last: Rainer

first: Federico

last: Sizzano

first: Nicola

last: Vannini


title: Gene expression of chronically UVA1-irradiated human dermal diploid fibroblasts

city: Quebec city

first: Patrick

last: Rochette

state: Quebec

address: 1050 chemin Ste-Foy - H2-10

department: Axe Médecine Régénératrice

country: Canada

institute: CHU de Québec – Université Laval

overall_design: Four normal human diploid fibroblasts strains were UVA-irradiated or not with 20 kJ/m^2 UVA, 2 times a day, 4 days a week for 5 weeks (40 X 20 kJ/m^2 , for a total of 800 kJ/m 2 UVA). Total RNA was extracted and analyzed

first: Alicia

last: Montoni

first: Kelly

last: George

first: Jérémie

last: Sœur

first: Christian

last: Tran

first: Laurent

last: Marrot


title: Dual inhibition of EZH1/2 depletes stem cells and over-activates WNT signaling in multiple myeloma

city: Durham

first: Makoto

last: Nakagawa

address: 308 Research Drive

department: Department of Orthopaedic Surgery

institute: Duke University

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

overall_design: Refer to individual Series


title: Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2 [I]

city: Houston

first: James

last: Lupski

state: TX

address: One Baylor Plaza Room #604B

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: Human genome structural variants (SVs) are caused by diverse mutational mechanisms. We used orthogonal long- and short-read sequencing technologies to investigate end products of de novo chromosome 17p11.2 rearrangements and query the molecular mechanisms underlying both recurrent and non-recurrent events. For non-recurrent events we found microhomology and microhomeology at the breakpoint junctions, an excess of deletion rearrangements on paternally-derived haplotypes, and elucidated recalcitrant breakpoints. Our data indicate an increased rate of clustered single nucleotide variant mutation in cis that is not present with recurrent rearrangement of the genome at the same locus. Indel and single nucleotide mutations are associated with both copy number gains and losses of 17p11.2, occur up to ~1 Mb away from the breakpoint junctions, and favor C>G transversion substitutions; results suggesting that single stranded DNA is formed during the genesis of the SV and providing compelling support for a microhomology-mediated break-induced replication mechanism for SV formation.

overall_design: To determine size, genomic extent and gene content for each rearrangement, we used a customized tiling-path oligonucleotide microarray spanning the 17p11.2 chromosomal region to query the genomic DNA of 55 individuals and their parents. This allowed us to discern the extent of the rearrangements, the copy number, and the de novo status of each rearrangement.

first: Christine

last: Beck


title: Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2 [II]


title: IL-15 Complex-Stimulated NK cells Protect Mice from Cerebral Malaria

city: Minneapolis

first: Sara

middle: Elizabeth

last: Hamilton Hart

state: MN

department: Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN

institute: University of Minnesota

summary: We report a comparison of purified mouse NK cells from mice treated in vivo with either IL-2 cytokine complexes or IL-15 cytokine complexes. We isolated RNA and performed HiSeq 2500 analysis on paired end reads of 125 base pairs in triplicate. We find relatively few significant gene expression changes between the groups, but discovered that IL-10 was induced with IL-15 cytokine complex treatment. We show that NK produced IL-10 rescues mice from lethal cerebral malaria.

overall_design: Sort purified splenic NK cells (NK1.1+NKp46+CD3-CD1d tetramer-) from female C57BL6 mice treated with either IL-2 cytokine complexes or IL-15 cytokine complexes

first: Kristina

middle: S

last: Burrack

first: Matthew

last: Huggins

first: Emily

last: Taras

first: Philip

last: Dougherty

last: Henzler

first: Rendong

last: Yang

first: Sarah

last: Alter

middle: K

last: Jeng

first: Hing

middle: C

last: Wong

first: Franck

last: Cichocki

first: Jeffrey

last: Miler

first: Geoffrey

middle: T

last: Hart

first: Aaron

last: Johnson

first: Stephen

last: Jameson

middle: E

last: Hamilton


title: Epithelial mesenchymal transition (EMT) in A549 NSCLC cells. TGFbeta was used to induce EMT, RNA isolated and subjected to RNAseq on Illumina HiSeq

first: John

last: Haley

state: NY

overall_design: Haley, J.A., Haughney, E., Ullman, E., Bean, J., Haley, J.D.* and Fink, M.Y. (2014) ‘Altered Transcriptional Control Networks with Trans-Differentiation of Isogenic Mutant KRas NSCLC Models’ Front. Oncology, doi/10.3389/fonc.2014.00344.

first: J

first: S

last: Thomson


title: Calcium signaling controls pathogenic Th17 cell-mediated inflammation by regulating mitochondrial metabolism

city: New York

first: Stefan

last: Feske

address: 550 First Avenue

institute: New York University School of Medicine

summary: Pathogenic Th17 cells play an important role in many autoimmune and inflammatory  diseases. Their function is dependent on signaling through the T cell receptor (TCR)  and cytokines that activate the transcription factor signal transducer and activator of  transcription 3 (STAT3). TCR engagement activates stromal interaction molecule 1  (STIM1) and calcium (Ca2+) influx through the Ca2+ release-activated Ca2+ (CRAC)  channel. We here show that deletion of STIM1 and Ca2+ influx in T cells expressing a  hyperactive form of STAT3 (STAT3C) attenuates pathogenic Th17 cell function and  multiorgan inflammation associated with STAT3C expression. Deletion of STIM1 in  pathogenic Th17 cells impairs the expression of nuclear encoded mitochondrial  electron transport chain genes and oxidative phosphorylation (OXPHOS) but enhances  reactive oxygen species (ROS) production. Deletion of STIM1 or inhibition of OXPHOS  is associated with impaired Th17 cell function and a non-pathogenic Th17 gene  expression signature. Our findings establish STIM1 and Ca2+ signals as a critical  regulator of OXPHOS and oxidative stress in pathogenic Th17 cells and multiorgan  inflammation.

overall_design: Comparing the transcriptome of in vitro differentiated pathogenic Th17 cells from Stat3CSTOPf/flCD4Cre and Stim1fl/flStat3CSTOPfl/flCD4Cre mice

first: Ulrike

last: Kaufmann


title: Enhancer Domains in Gastrointestinal Stromal Tumor Regulate KIT Expression and are Targetable by BET Bromodomain Inhibition

last: Hemming


title: sRNA sequencing of miRNAs in primary human islets

status: Public on Jan 16 2019

city: Nashville

first: Leslie

middle: Roteta

last: Sedgeman

state: TN

address: 2220 Pierce Avenue

institute: Vanderbilt University

summary: miRNAs are exported to high density lipoproteins (HDL). This study aimed to understand what miRNAs are present in primary human islets from 1 donor

overall_design: Examination of miRNAs in primary islets

first: Kasey

last: Vickers


title: sRNA sequencing of miRNAs exported to HDL from INS-1 rat insulinoma cells

summary: miRNAs are exported to high density lipoproteins (HDL). This study aimed to understand what miRNAs are exported from INS-1 cells to HDL in vitro.

overall_design: Examination of miRNAs exported from INS1 cells to HDL


title: Single cell RNAseq analysis of Col2a1+ growth plate chondrocytes

first: Noriaki

last: Ono

state: Texas

department: School of Dentistry

institute: University of Texas Health Science Center at Houston

summary: We set out to reveal single cell transcriptional profiles of neonatal growth plate chondrocytes

overall_design: tdTomato+ cells were FACS-isolated from postnatal day 2 (P2) growth plates of Col2a1-creER; R26R-tdTomato+ femurs (tamoxifen at P0). 18,000 cells were loaded onto 10X Genomic Chromium platform. cDNA was sequenced by Illumina HiSeq4000.


title: A Machine Learning Classifier for Assigning Individual Patients with Systemic Sclerosis to Intrinsic Molecular Subsets

status: Public on Jan 19 2019

city: Lebanon

first: Tammara

last: Wood

state: NH

address: WTRB 674

department: Biomedical Data Science

institute: Dartmouth Medical School

summary: DNA microarray and RNA-seq were performed on samples from four controls and eight SSc patients for testing the performance of intrinsic subset classification in two different gene expression profiling platforms. N0901, N0903, N1002, N1003, SSc0882, SSc0916, SSc0918, S0920 have previously been deposited on NCBI SRA at PRJNA237826. The remaining four SSc RNA-seq samples will be available at PRJNAXXXXXX.

overall_design: Microarray gene expression and intrinsic subset assignment were measured in 8 SSc patient and 4 control biopsies


title: Next-Generation Sequencing Facilitates Centromere Position Analysis of Gossypium barbadense and Gossypium hirsutum

city: Fuzhou

first: Zhiliang

last: Zhang

address: Shangxiadian

institute: Fujian Agriculture and Forestry University

summary: We conduct a genome-wide analysis of the DNA sequences associated with CenH3 using chromatin immunoprecipitation to map the position of centromere regions.

sample_organism:
Gossypium barbadense
Gossypium hirsutum

platform_organism:
Gossypium barbadense
Gossypium hirsutum

first: Kai

last: Wang


title: SpyCLIP: An easy-to-use and high-throughput compatible platform for efficient characterization of protein-RNA interactions

status: Public on Jan 21 2019

city: Shanghai

first: Ligang

last: Wu

state: Shanghai

address: 320 Yueyang Road

department: Shanghai Institutes for biological Sciences

institute: Chinese Academy of Sciences

summary: We have developed a covalent linkage-based SpyCLIP method by taking advantage of SpyTag-SpyCatcher chemistry, which circumvents gel purification steps of captured RBP-RNA needed for all existing CLIP methods, thereby dramatically reducing the technical difficulty and enabling high-throughput application of the CLIP technology.

overall_design: SpyCLIP and corresponding input sample for PTBP1, SLBP, RBFOX2 and AGO2 in Lenti-X 293T cell line.

first: Ya

last: Zhao

first: Yao

first: Yilan

last: Teng

last: Liu

first: Yanqing

first: Weihua

last: Li


title: A miRNA-mediated approach to dissect the complexity of tumor-initiating cell function and identify miRNA-targeting drugs

city: Ann Arbor

first: Analisa

last: DiFeo

state: MI

address: 1600 Huron Parkway

department: Pathology

institute: The University of Michigan

summary: Microarray analysis of miR-181a sensor sorted primary HGSOC cells to determine the ability of miRNA sensor to regulate various cancer related pathways.

overall_design: Total RNA was extracted from cell lysates of OCI-P5X miR-181a high and OCI-P5X miR-181a low cells in triplicate and Affymetrix Human Clariom S array and the WT Plus chemistry was performed


title: Enhancer Domains in Gastrointestinal Stromal Tumor Regulate KIT Expression and are Targetable by BET Bromodomain Inhibition [RNA-seq]

first: Matthew

overall_design: RNA-seq from GIST cell lines treated with drug or DMSO control.


title: Loss of miR-210 leads to progressive retinal degeneration in Drosophila melanogaster

status: Public on Jan 18 2019

city: South San Francisco

first: Oliver

last: Hahn

state: CA

address: 1170 Veterans Blvd

institute: Calico Life Sciences, LLC

summary: miRNAs are small, non-coding RNAs that regulate gene expression post-transcriptionally. We used small RNA sequencing to identify tissue-specific miRNAs in the adult brain, thorax, gut and fat body of Drosophila melanogaster. One of the most brain-specific miRNAs that we identified was miR-210, an evolutionarily highly conserved miRNA implicated in the regulation of hypoxia in mammals. In Drosophila, we show that miR-210 is specifically expressed in sensory organs including photoreceptors. miR-210 knock-out mutants are not sensitive towards hypoxia but show progressive degradation of photoreceptor cells, accompanied by decreased photoreceptor potential, demonstrating an important function of miR-210 in photoreceptor maintenance and survival.

overall_design: Multi-tissue miRNA-seq in wild type D. melanogaster to identify tissue-specific miRNAs. RNA-seq of miR-210 knockout fly heads to identify potential targets.

first: Carina

last: Weigelt

first: Katharina

last: Arlt

first: Matthias

last: Gruhn

first: Jacqueline

last: Eßer

first: Jennifer

last: Werner

first: Corinna

last: Klein

first: Ansgar

last: Büschges

first: Sebastian

last: Grönke

first: Linda

last: Partridge


title: CG dinucleotides enhance promoter activity independent of DNA methylation

status: Public on Jan 20 2019

city: Basel

first: Dirk

last: Schuebeler

address: Fabrikstrasse 24

institute: Friedrich Miescher Institute for Biomedical Research

summary: Most mammalian RNA Polymerase II initiation events occur at CpG islands, which are rich in CpGs and devoid of DNA methylation. Despite their relevance for gene regulation, it is unknown to what extent the CpG dinucleotide itself actually contributes to promoter activity. To address this question, we determined the transcriptional activity of a large number of chromosomally integrated promoter constructs and monitored binding of transcription factors assumed to play a role in CpG island activity. This revealed that CpG density significantly improves motif-based prediction of transcription factor binding. Our experiments also show that high CpG density alone is insufficient for transcriptional activity, yet results in increased transcriptional output when combined with particular transcription factor motifs. Yet, this CpG contribution to promoter activity is independent of DNA methyltransferase activity. Together this refines our understanding of mammalian promoter regulation as it shows that high CpG density within CpG islands directly contributes to an environment permissive for full transcriptional activity.

overall_design: We monitored binding of transcription factors assumed to play a role in CpG island activity using ChIPseq and tested expression of a large number of promoter mutants, including artificial promoter sequences, when inserted into the genome using a novel high throughput transcriptional reporter assay.

first: Dominik

last: Hartl

first: Arnaud

middle: R

last: Krebs

first: Ralph

last: Grand

first: Tuncay

last: Baubec

first: Luke

last: Isbel

first: Christiane

last: Wirbelauer

first: Lukas

last: Burger

last: Schübeler


title: Transcriptional profiling of PPARα-/- and CREB3L3-/- livers reveals disparate regulation of hepatoproliferative and metabolic functions of PPARα

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Peroxisome Proliferator-Activated receptor α (PPARα) and cAMP-Responsive Element Binding Protein 3-Like 3 (CREB3L3) are transcription factors involved in the regulation of lipid metabolism in the liver. The aim of the present study was to characterize the interrelationship between PPARα and CREB3L3 in regulating hepatic gene expression. Male wildtype, PPARα-/-, CREB3L3-/- and combined PPARα/CREB3L3-/- mice were subjected to a 16-hour fast or 4 days of ketogenic diet. Whole genome expression analysis was performed on liver samples. Under conditions of overnight fasting, the effects of PPARα ablation and CREB3L3 ablation on plasma triglyceride, plasma β-hydroxybutyrate, and hepatic gene expression were largely disparate, and showed only limited interdependence. Gene and pathway analysis underscored the importance of CREB3L3 in regulating (apo)lipoprotein metabolism, and of PPARα as master regulator of intracellular lipid metabolism. A small number of genes, including Fgf21 and Mfsd2a, were under dual control of PPARα and CREB3L3. By contrast, a strong interaction between PPARα and CREB3L3 ablation was observed during ketogenic diet feeding. Specifically, the pronounced effects of CREB3L3 ablation on liver damage and hepatic gene expression during ketogenic diet were almost completely abolished by the simultaneous ablation of PPARα. Loss of CREB3L3 influenced PPARα signalling in two major ways. Firstly, it reduced expression of PPARα and its target genes involved in fatty acid oxidation and ketogenesis. In stark contrast, the hepatoproliferative function of PPARα was markedly activated by loss of CREB3L3. These data indicate that CREB3L3 ablation uncouples the hepatoproliferative and lipid metabolic effects of PPARα. Overall, except for the shared regulation of a very limited number of genes, the roles of PPARα and CREB3L3 in hepatic lipid metabolism are clearly distinct and are highly dependent on dietary status.

overall_design: Wildtype, PPARα-/-, CREB3L3-/- and combined PPARα/CREB3L3-/- mice were subjected to a 16-hour fast or 4 days of ketogenic diet, whereafter their livers were subjected to gene expression profiling.

first: Philip

last: Ruppert

first: Jong-Gil

last: Park

first: Xu

last: Xu

first: Kye

middle: Y

last: Hur

first: Ann-Hwee

last: Lee

first: Sander

last: Kersten


title: Contrasting roles of the RSC and ISW1/CHD1 chromatin remodelers in RNA polymerase II elongation and termination

city: Bethesda

first: Razvan

middle: V.

last: Chereji

state: Maryland

address: 6 Center Drive, Room 2A14

department: NICHD

institute: National Institutes of Health

summary: Most yeast genes have a nucleosome-depleted region (NDR) at the promoter and an array of regularly spaced nucleosomes phased relative to the transcription start site. We have examined the interplay between RSC (a conserved essential SWI/SNF-type complex that determines NDR size) and the ISW1, CHD1 and ISW2 nucleosome spacing enzymes in chromatin organization and transcription, using isogenic strains lacking all combinations of these enzymes. The contributions of these remodelers to chromatin organization are largely combinatorial, distinct and non-redundant, supporting a model in which the +1 nucleosome is positioned by RSC and then used as a reference nucleosome by the spacing enzymes. Defective chromatin organization correlates with altered RNA polymerase II (Pol II) distribution. RSC-depleted cells exhibit low levels of elongating Pol II and high levels of terminating Pol II, consistent with defects in both termination and initiation, suggesting that RSC facilitates both. Cells lacking both ISW1 and CHD1 show the opposite Pol II distribution, suggesting elongation and termination defects. These cells have extremely disrupted chromatin, with high levels of close-packed di-nucleosomes near the 5’-ends of genes. We propose that ISW1 and CHD1 facilitate Pol II elongation by separating close-packed nucleosomes and by eliminating long linkers to prevent cryptic initiation.

overall_design: MNase-seq data from two biological replicate experiments (one experiment with 2 levels of MNase digestion, the other with one level of digestion): MNase digestion of nuclei from wild type (WT) and isw1∆ chd1∆ double mutant cells

first: Josefina

last: Ocampo

middle: V

first: Peter

last: Eriksson

first: David

middle: J

last: Clark


title: Suppression of ILC2 differentiation from committed T cell precursors by E protein transcription factors

city: Oklahoma City

first: Jonathan

last: Wren

state: OK

address: 825 N.E. 13th Street

department: Genes & Human Disease Research Program

institute: OMRF

summary: Current models propose that group 2 innate lymphoid cells are generated in the bone marrow. Here we demonstrate that subsets of these cells can differentiate from multipotent progenitors and committed T cell precursors in the thymus, both in vivo and in vitro.  These thymic ILC2s can exit the thymus, circulate in the blood and home to peripheral tissues.  Ablation of E protein transcription factors greatly promotes the innate lymphoid cell fate at the expense of B and T cell development.  Consistently, a transcriptional network centered on the ZBTB16 transcription factor and IL-4 signaling pathway is highly up-regulated due to E protein deficiency.  Our results show that ILC2 can still be generated from what are normally considered to be committed T cell precursors, and that this alternative cell fate is restrained by high levels of E protein activity in these cells.

overall_design: RNA-seq was performed on freshly isolated ILC2 cells from the thymus, mesenteric lymph nodes and lung of different strains of mice.  Cells cultured from DN1 or DN3 thymocytes on OP9-DL1 stromal cells in the presence IL-2, IL-7 and Stem cell factor were also analyzed. The genotypes of the mice where DN1 and DN3 cells were obtained are ROSA26-CreERT2;ROSA26-stop-tdTomato and ROSA26-CreERT2;ROSA26-stop-tdTomato;E2Af/f/HEBf/f.  Addition of tamoxifen on Day 4 to the cultures induces deletion of the HEB and E2A gene as well as the expression of tdTomato.  On Day 5 and Day7 of the culture, tdTomato positive cells were sorted and used for RNA isolation.

first: Xiao-Hong

last: Sun

first: Constantin

last: Georgescu

first: Indra

last: Adrianto


title: MS2-affinity purification coupled with RNA sequencing (MAPS) reveals SraL sRNA targetome in Salmonella Typhimurium

city: SHERBROOKE

first: Eric

last: Massé

state: Québec

address: 3201, Jean Mignault

department: Biochemistry

institute: University of Sherbrooke

summary: Recently, we developed an in vivo technology to draw the interacting map of a specific small regulatory RNA (sRNA). We called it MAPS for MS2-affinity purification coupled with RNA sequencing. In this study, we performed MAPS with SraL sRNA (Salmonella Typhimurium SL1344).

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. SL1344

overall_design: Identification of RNAs co-purified with MS2-SraL in a sraL- strain. SraL (without MS2) was used as control.

first: Alex

last: Eyraud

last: Lalaouna


title: Megabase Length Hypermutation Accompanies Human Structural Variation at 17p11.2

first: James

last: Lupski

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

overall_design: Refer to individual Series


title: Functional Genomics Screen with Pooled shRNA Library and Gene Expression Profiling with Extracts of Azadirachta indica Identify Potential Pathways for Therapeutic Targets in Head and Neck Squamous Cell Carcinoma

status: Public on Jan 15 2019

city: new delhi

first: binay

last: panda

address: 1649A vasant kunj

institute: ganit labs foundation

summary: We investigate the molecular targets and pathways that the neem extracts and the associated compounds act through, to bring about tumor suppression by using a genome-wide functional pooled shRNA screen on head and neck squamous cell carcinoma cell line treated with crude neem leaf extracts. We analyzed differences in global clonal sizes of the shRNA-infected cells cultured under no treatment and treatment with neem leaf extract conditions, assayed using next-generation sequencing. We further analyzed differences in gene expression in HSC-4 cells, upon treatment with neem leaf extract in a time-dependent manner, followed by a time-dependent rescue. Our results indicate that neem extract simultaneously affects various important molecular signaling pathways in head and neck cancer cells, some (TGF-β/HSF-1) of which may be therapeutic targets for this devastating tumor.

overall_design: RNA was extracted from HSC-4 cells, seeded and treated with neem leaf extract (200μg/ml) at nine pre-defined time points (5min, 10min, 15min, 30min, 1hr, 3hr, 6hr, 10hr, and 24hr) and rescued with fresh complete medium post 48-hour treatment at these time-points. The samples were assayed for gene expression using Illumina whole-genome HumanHT-12 v4 expression BeadChip (Illumina, San Diego, CA), following the manufacturer’s specifications.

first: Manisha

last: Pareek

first: Vinayak

last: Palve

first: Neeraja

last: Krishnan

first: Binay

last: Panda


title: Targeting EZH2 increases the vulnerability of triple-negative breast cancer

city: Leuven

first: Jieyi

last: Xiong

address: Herestraat 49, box 912

country: Belgium

institute: VIB-KULeuven Center for Cancer Biology

summary: We hypothesize that knockdown or inhibition of the EZH2 results in decreased proliferation and tumorigenic potential of TNBC breast cancer cells

overall_design: Examination of gene expression in three TNBC breast cancer cell lines following knockdown of EZH2 or chemical inhibition of EZH2 activity

first: Yong

last: Yu

first: Jingjing

last: Qi

first: Liping

last: Jiang

first: Clemens

last: Schmitt

first: Ran

last: Tao