title: Oral vitamin D for the attenuation of sunburn

city: Cleveland

first: Kurt

last: Lu

state: OH

address: 2109 Adelbert Road

department: Dermatology

institute: Case Western Reserve University/ University Hospitals Case Medical Ctr

summary:
Background: The diverse immunomodulatory effects of vitamin D are increasingly being recognized. However, the ability of oral vitamin D to modulate immune responses in vivo has not been established in humans. Methods: Twenty healthy adults were randomized to receive placebo or a single high dose of vitamin D3 (cholecalciferol) one hour after localized skin irradiation with an erythemogenic dose of ultraviolet radiation. Primary outcomes included skin redness, skin thickness, and tissue expression of inflammatory mediators (TNF-α and iNOS). Secondary outcomes included microarray analyses. Results: As compared to placebo, subjects receiving vitamin D3 (200,000 IU) demonstrated reduced expression of TNF-α (p=0.04) and iNOS (p=0.02) in skin biopsies 48 hours after ultraviolet light exposure. Demonstrated trends included reduced skin redness (p=0.17), and reduced skin thickness (p=0.09) in subjects receiving vitamin D3 (200,000 IU). Unsupervised clustering of individuals based on global gene expression revealed that subjects with enhanced skin barrier repair expression profiles had higher serum vitamin D3 levels (p=0.007), increased arginase expression (p=0.005), and a sustained reduction in skin redness (p=0.02) after treatment, as compared to subjects with enhanced inflammatory gene expression profiles.
Conclusions: A single high dose of oral vitamin D is capable of attenuating a local sunburn response to ultraviolet radiation, suggesting that oral vitamin D may be clinically therapeutic for its immunomodulatory properties. These results have broad implications for the role of vitamin D in skin homeostasis, and implicate arginase activation as a novel mechanism by which vitamin D exerts anti-inflammatory effects in humans.

overall_design: Twenty healthy adults were randomized to receive placebo or a single high dose of vitamin D3 (cholecalciferol) one hour after localized skin irradiation with an erythemogenic dose of ultraviolet radiation. Four treatment groups were defined. There were 4 subjects in the placebo group (8 paired samples after SSR, 4 with and 4 without placebo), 5 subjects  in the 50,000IU Vitamin D3 treatment group (10 paired samples, 5 with and 5 without treatment), 4 subjects in the 100,000IU Vitamin D3 treatment group (8 paired samples, 4 with and 4 without treatment), and 5 subjects in the 200,000IU Vitamin D3 treatment group (10 paired samples, 5 with and 5 without treatment). 5 skin samples came from non-irradiated controls.

first: J

middle: F

last: Scott

first: L

last: Das

first: S

last: Ahsanuddin

first: Y

last: Qui

first: A

last: Binko

first: Z

middle: P

last: Traylor

last: Debanne

first: K

last: Cooper

first: R

last: Boxer


title: Peritoneal cavity macrophage response to IFNg and IFNa

status: Public on Feb 14 2018

city: Boston

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

country: USA

institute: Harvard Medical School

summary: We seeked to determine in vivo effects of IFNg and IFNa response in peritoneal cavity macrophages. These cells were part of ImmGen Interferon cytokine study and immunocytes were sorted according to Immgen's standard lineage panel. Profiles from peritoneal cavity macrophages were used to analyze cell specific responses to IFNg.

overall_design: 8,000 units of recombinant IFNg or 10,000 units of recombinant IFNa were injected subcutaneously in C57bl6 6-week-old male mice. Mice were sacrificed 2 hours after injection and peritoneal lavage was collected. F4/80+ ICAM+ peritoneal cavity macrophages were double sorted using FACSAria into Trizol.

first: Marisella

last: Panduro

first: Adriana

last: Ortiz-Lopez

first: Andrew

last: Rhoads

first: Devan

last: Moodley

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Single cell transcriptomic analysis (InDrops) of mouse FoxP3- CD4+ Tconv cells and FoxP3+ regulatory CD4+ T cells isolated from spleen and visceral adipose tissue

status: Public on Feb 16 2018

type: Expression profiling by high throughput sequencing

overall_design: Single cells were sorted by flow cytometry for single cell RNAseq library preparation (InDrops)

first: David

last: Zemmour


title: Single-Cell RNA Sequencing Reveals Metallothionein Heterogeneity during hESC Differentiation to Definitive Endoderm [RNA-Seq]

status: Public on Feb 15 2018

city: Rochester

first: Hu

last: Li

state: MN

address: 200 First Street, Gonda Building G19-408

department: Molecular Pharmacology & Experimental Therapeutics

institute: Mayo Clinic

summary: Differentiation of human pluripotent stem cells toward definitive endoderm (DE) is the critical first step for generating cells comprising organs such as the gut, liver, pancreas and lung. This in-vitro differentiation process generates a heterogeneous population with a proportion of cells failing to differentiate properly and maintaining expression of pluripotency factors such as Oct4. RNA sequencing of single cells collected at four time points during a 4-day DE differentiation identified high expression of metallothionein genes in the residual Oct4-positive cells that failed to differentiate to DE. Using X-ray fluorescence microscopy and multi-isotope mass spectrometry, we discovered that high intracellular zinc level corresponds with persistent Oct4 expression and failure to differentiate. This study improves our understanding of the cellular heterogeneity during in-vitro directed differentiation and provides a valuable resource to improve DE differentiation efficiency.

overall_design: H9 human ES cells undergoing DE differentiation were collected daily (day 0-4) for RNA sequencing. Experiments were performed in triplicates.

first: Junjie

last: Lu

first: Paul

last: Lerou


title: Tuberous sclerosis complex-associated CNS abnormalities depend on hyperactivation of mTORC1 and Akt

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

summary: Tuberous sclerosis complex (TSC) is a dominantly inherited disease, caused by hyperactivation of the mTORC1 pathway and characterized by the development of hamartomas and benign tumors, also in the brain. Among the neurological manifestations associated with TSC, the tumor progression of static subependymal nodules (SENs) into subependymal giant cell astrocytomas (SEGAs) is one of the major causes of morbidity and shortened life expectancy. To date, mouse modeling has failed in reproducing these two lesions. Here we report that simultaneous hyperactivation of mTORC1 and Akt pathways by co-deletion of Tsc1 and Pten, selectively in postnatal neural stem cells (pNSCs), is required for the formation of bona fide SENs and SEGAs. Notably, both lesions closely recapitulate the pathognomonic morphological and molecular features of the corresponding human abnormalities. The establishment of long-term expanding pNSC lines from mouse SENs and SEGAs made possible the identification of mTORC2 as one of the mediators conferring tumorigenic potential to SEGA pNSCs. Of note, in spite of concurrent Akt hyperactivation in mouse brain lesions, single mTOR inhibition by rapamycin was sufficient to strongly impair mouse SEGA growth. This study provides the first evidence that, concomitant with mTORC1 hyperactivation, sustained activation of Akt and mTORC2 in pNSCs is a mandatory step for the induction of SENs and SEGAs and, at the same time, makes available an unprecedented NSC-based in vivo/in vitro model to be exploited for identifying actionable targets in TSC.

overall_design: Comparison of the gene expression profile of pNSC-derived subcutaneous tumors with that of control pNSCs.

middle: M

first: Paola

last: Zordan

first: Rossella

last: Galli


title: Interferon Gamma mRNA Signature in Tumor Biopsies Predicts Outcomes in Patients with Non–Small-Cell Lung Carcinoma or Urothelial Cancer Treated with Durvalumab

city: Gaithersburg

first: Yinong

last: Sebastian

address: One MedImmune Way

institute: Medimmune

summary: An unmet need in cancer treatment is identification of biomarkers of response to PD-1 or PD-L1 immune checkpoint inhibitors that predict therapeutic outcomes in patients with non–small-cell lung carcinoma (NSCLC) and urothelial cancer (UC). Expression of PD-L1 measured by immunohistochemistry has limited capacity for predicting outcomes of immune checkpoint therapy because expression of this biomarker does not correlate highly with treatment response. In addition, PD-L1 as measured on tumor cells, which has been approved by the FDA for both companion and complementary diagnostic utility, does not necessarily reflect anti-tumor activity of tumor-infiltrating lymphocytes. Results presented in this report demonstrate that gene expression levels of four interferon gamma (IFNγ)-inducible mRNAs correlate with improved clinical outcomes in patients with NSCLC or UC treated with the PD-L1 inhibitor durvalumab. This IFNγ gene signature may augment the predictive value of PD-L1 and other biomarkers in identifying cancer patients most likely to respond to therapy with durvalumab or other immune checkpoint inhibitors.

overall_design: RNA sequencing of 97  biopsies from a nonrandomized phase 1b/2 clinical trial (1108/NCT01693562) were profiled to identify a predictive signature; 62 locally advanced or metastatic urothelial cancer (UC) tumors from the same study were profiled to confirm predictive utility of the signature.

first: Brandon

middle: W

last: Higgs


title: Mouse bone marrow inDrop

first: Peter

last: Kharchenko

address: 10 Shattuck St.

department: DBMI

summary: Single-cell RNA-seq measurements of the normal mouse bone marrow cells using inDrop protocol

overall_design: Whole bone marrow cells were isolated from the C57Bl/6 mice. The single-cell RNA-seq library was prepared using inDrop approach and sequenced using Illumina Next-seq 500.

first: Jimin

last: Guo


title: Single cell transcriptomic analysis (InDrops) of FoxP3+ regulatory CD4+ T cells isolated from the spleen and visceral adipose tissue of wild-type and VAT-TCR transgenic mice

first: CBDM

last: Lab

first: Chaoran


title: Immune-Responsive Gene 1 expression in myeloid cells prevents neutrophil mediated immunopathology during Mycobacterium tuberculosis infection [macrophage]

first: Maxim

middle: N.

last: Artyomov

state: MO

address: 660 S. Euclid Avenue, Campus Box 8118

department: Immunology&Pathology

institute: Washington University in St.Louis

summary: Immune-Responsive Gene 1 (Irg1) is a mitochondrial enzyme that produces itaconate under inflammatory conditions principally in cells of myeloid lineage. Cell culture studies suggest that itaconate regulates inflammation through inhibitory effects on cytokine and reactive oxygen species production. To evaluate the functions of Irg1 in vivo, we challenged wild-type (WT) and Irg1-/- mice with Mycobacterium tuberculosis (Mtb) and monitored disease progression. Irg1-/- but not WT mice succumbed rapidly to Mtb, and mortality was associated with increased infection, inflammation, and pathology. Infection of LysM-Cre Irg1fl/fl, MPR8-Cre Irg1fl/fl, and CD11c-Cre Irg1fl/fl conditional knockout mice along with neutrophil depletion experiments revealed a role for Irg1 in alveolar macrophages and LysM+ myeloid cells in preventing neutrophil-mediated immunopathology and disease. RNA-seq analyses suggest that Irg1 and its production of itaconate temper Mtb-induced inflammatory responses in myeloid cells at the transcriptional level. Thus, Irg1 modulates inflammation to curtail Mtb-induced lung disease.

overall_design: Macrophages were obtained by culturing bone marrow cells in RPMI-1640 (Invitrogen) supplemented with 10% heat inactivated fetal bovine serum, 2 mM L-glutamine, 1% non-essential amino acids, 100 U penicillin per mL, 100 μg streptomycin per mL, and 22 ng M-CSF (Peprotech) per ml for 6 days at 37°C, 5% CO2. Fresh media was added on day 3 of culture. After 6 days of culture, non-adherent cells were discarded. Adherent macrophages were switched into antibiotic-free media and seeded at 105 cells per well and 9 x 105 cells per well in tissue culture-treated 96 and 6 well plates respectively. In some cases, macrophages were treated with 0.25 mM itaconic acid (Sigma) for 12 h prior to inoculation with Mtb. Mtb was grown to mid-log phase, washed with PBS, sonicated to disperse clumps, and resuspended in antibiotic-free macrophage culture media. Macrophage cultures were inoculated by adding Mtb-containing media at a multiplicity of infection (MOI) of 1 and centrifuging for 10 min at 200 x g. Cells were washed twice with PBS to remove unbound Mtb, fresh culture media was added, and cells were incubated at 37°C, 5% CO2. In some cases culture media was supplemented with 0.25 mM itaconic acid.

first: Sharmila

last: Nair

first: Jeremy

last: Hyunh

first: Vicky

last: Lampropoulou

first: Ekaterina

last: Esaulova

last: Loginicheva

first: Anshu

last: Gounder

first: Adrianus

middle: C

last: Boon

first: Elizabeth

middle: A

last: Schwarzkopf

first: Tara

middle: R

last: Bradstreet

first: Brian

middle: T

last: Edelson

middle: N

first: Christina

middle: L

last: Stallings

first: Michael

middle: S

last: Diamond


title: Single cell transcriptomic analysis (InDrops) of mouse FoxP3- CD4+ Tconv cells and FoxP3+ regulatory CD4+ T cells isolated from secondary lymphoid organs

first: David

last: Zemmour

first: Christophe

last: Benoist


title: Single cell transcriptomic analysis (InDrops) of mouse splenic FoxP3+ regulatory CD4+ T cells isolated from different bins of Nr4a1-GFP expression


title: secondary structure based on icSHAPE of pre-let-7 and hDicer-TRBP  bound pre-let-7

city: Qingdao

first: Lei

last: Sun

state: Shandong

address: Shandong street

country: China

institute: Shandong University

summary: we resolved precusor let7 (pre-let-7) and human Dicer-TRBP complex bound precusor let7 (hDicer-TRBP-pre-let-7) secondary structure based on  in vivo click selective 2'-hydroxyl acylation and profiling experiment (icSHAPE). We found the free pre-let-7 RNA is more flexible comparing with hDicer-TRBP-pre-7 in the double strand region [10-20nt and 50- 60 nt].

overall_design: The pre-let-7 RNA (5ʹ-UGAGGUAGUAGGUUGUAUAGUUUUAGGGUCACACCCACCACUGGGAGAUAACUAUACAAUCUACUGUCUUACC-3ʹ) was synthesized by Genescript Inc. In order to form the hairpin pre-let-7, we heated the RNA at 90 °C for 3 min then snap-cooled it on ice for 5 min. In order to reconstitute the hDicer-TRBP-pre-let-7 complex, we mixed ~200 µg (0.8 nmol) hDicer-TRBP complex and ~54 µg (2.3 nmol) pre-let-7 RNA in 50 µl of gel filtration buffer containing 2 mM Ca2+ and incubated the mixture on ice for 40 min. After this, the mixture was applied to a Superose™ 6 Increase 5/150 GL (GE Healthcare) column installed on an ÄKTAmicro (GE Healthcare) equilibrated in gel filtration buffer containing 2 mM Ca2+. Fractions containing the hDicer-TRBP-pre-let-7 complex were collected at a final concentration of ~0.4 mg/ml. NAI-N3 modified the free pre-let-7 and hDicer-TRBP-pre-let-7 complex for 10 min in 37°C. then the RNA are purified and building library as the icSHAPE protocol.

first: Qiangfeng

last: Zhang


title: Rif1 acts through Protein Phosphatase 1 and independent of replication timing to suppresses telomere extension in budding yeast

city: Norwich

first: Conrad

last: Nieduszynski

address: Norwich Research Park

country: United Kingdom

institute: Earlham Institute

summary: The Rif1 protein negatively regulates telomeric TG repeat length in the budding yeast S. cerevisiae, but how it prevents telomere over-extension is unknown. Rif1 was recently shown to control DNA replication by acting as a Protein Phosphatase 1 (PP1)-targeting subunit. Therefore we investigated whether Rif1 controls telomere length by targeting PP1 activity. We find that a Rif1 mutant that cannot interact with PP1 causes a long-telomere phenotype, similar to that of rif1∆ cells. Compromised PP1 function also causes telomere extension. Tethering PP1 at a specific telomere partially substitutes for Rif1 in limiting TG repeat length, confirming the importance of PP1 in telomere length control. Ablating Rif1-PP1 interaction leads to precocious activation of telomere-proximal replication origins and aberrantly early telomere replication. However, we find that Rif1 still limits telomere length even if nearby replication origins are deleted, indicating that effects of Rif1 on telomere length are not mediated through replication timing. Instead we find that, even at a telomere created after DNA synthesis during a mitotic block, Rif1-PP1 interaction is required to suppress telomere lengthening and prevent inappropriate recruitment of Tel1 kinase. Overall, our results show that Rif1 controls telomere length by recruiting PP1 to directly suppress telomerase-mediated TG repeat lengthening.

overall_design: Saccharomyces cerevisiae strains were arrested in G1 with alpha-factor before being released into S-phase. Copy number was measured by NGS at various timepoints into S-phase, as a proxy for replication timing.

first: Sylwia

last: Kedziora

first: Shin-ichiro

last: Hiraga

first: Kate

last: Clark

first: Rosemary

last: Wilson

first: Anne

middle: D

last: Donaldson


title: Inhibition of the kinesin spindle protein enhances the activity of pomalidomide and dexamethasone in multiple myeloma [In Vitro]

city: Salamanca

first: Enrique

middle: M.

last: Ocio

state: Salamanca

address: Campus Universitario Miguel de Unamuno

country: Spain

institute: Centro de investigación del cáncer

summary: Kinesin spindle protein (KSP) inhibition is known to be an effective therapeutic approach in several malignancies. Filanesib (Arry-520), a KSP inhibitor, has demonstrated activity in heavily pretreated multiple myeloma (MM) patients. The aim of this work was to investigate the activity of filanesib in combination with an IMiDs plus dexamethasone backbone, and the mechanisms underlying the potential synergistic effect. Results: Filanesib showed in vitro and in vivo synergy with all IMiDs plus dexamethasone treatment, particularly with the pomalidomide combination (PDF). Importantly, the in vivo synergy observed in this combination was more evident in large, highly proliferative tumors, and it was shown to be mediated by impairment of mitosis transcriptional control, an increase in monopolar spindles, cell cycle arrest and the induction of apoptosis in cells in proliferative phases. In addition, PDF increased the activation of the proapoptotic protein Bax, which has been previously associated with sensitivity to filanesib, and could potentially be used as a predictive biomarker of response to this combination.   Conclusions: Our results provide preclinical evidence for the potential benefit of the combination of filanesib with pomalidomide and dexamethasone and es-tablished the basis for a recently activated trial being conducted by the Spanish MM group investigating this combination in relapsed MM patients.

overall_design: The ability of filanesib to enhance the activity of the different IMiDs plus dexamethasone was compared in several in vitro and in vivo models. Mechanisms of the most synergistic combination were dissected by gene expression profiling, immunostaining, cell cycle and siRNA studies

first: Susana

last: Hernández-García

first: Laura

last: San-Segundo

first: Lorena

last: González-Méndez

first: Luis

last: Corchete

first: Irena

last: Misiewicz-Krzeminska

first: Montserrat

last: Martín-Sánchez

first: Ana-Alicia

last: López-Iglesias

first: Esperanza

last: Algarín

first: Teresa

last: Paíno

last: Tunquist

first: María-Victoria

last: Mateos

first: Norma

last: Gutiérrez

first: Elena

last: Díaz-Rodriguez

first: Mercedes

last: Garayoa


title: DNA methylation, through DNMT1, has an essential role in the development of gastrointestinal smooth muscle cells and disease (BiSulfite-seq)

status: Public on Feb 13 2018

city: Reno

first: Seungil

last: Ro

state: NV

address: 1664 North Virginia St

department: Physiology and Cell Biology

institute: University of Nevada School of Medicine

type: Methylation profiling by high throughput sequencing

summary: DNA methylation is a key epigenetic modification that can regulate gene expression. Genomic DNA hypomethylation is commonly found in many gastrointestinal (GI) diseases. Dysregulated gene expression in GI smooth muscle cells (GI-SMC) can lead to motility disorders. However, the consequences of genomic DNA hypomethylation within GI-SMC are still elusive. Utilizing a Cre-lox murine model, we have generated SMC-restricted DNA methyltransferase 1 (Dnmt1) knockout (KO) mice and analyzed the effects of Dnmt1 deficiency. Dnmt1-KO pups are born smaller than their wild type littermates, have shortened GI tracts, lose peristaltic movement due to loss of the tunica muscularis in their intestine, causing massive intestinal dilation, and death around post-natal day 21. Within smooth muscle tissue, significant CpG hypomethylation occurs across the genome at promoters, introns and exons. Additionally, there is a marked loss of differentiated SMC markers (Srf, Myh11, miR-133, miR-143/145), an increase in pro-apoptotic markers (Nr4a1, Gadd45g), loss of cellular connectivity, and an accumulation of coated vesicles within SMC. Interestingly, we observed consistent abnormal expression patterns of enzymes involved in DNA methylation between both ¬Dnmt1-KO mice and diseased human GI tissue. These data demonstrate that DNA hypomethylation in embryonic SMC, via congenital Dnmt1 deficiency, contributes to massive dysregulation of gene expression and is lethal to GI-SMC. These results suggest that Dnmt1 has a necessary role in the embryonic, primary development process of SMC with consistent patterns being found in human GI diseased tissue.

overall_design: mRNA and DNA methyation profiles of Dnmt1 WT and KO  jejunum smooth muscle were generated by deep sequencing using Illumina Hiseq2000.

first: Brian

middle: G

last: Jorgensen

first: Robyn

last: Berent

first: Se

middle: E

last: Ha

first: Kazuhide

last: Horiguchi

first: Kent

last: Sasse

first: Laren

last: Becker


title: Tissue- and strain-specific effects of a genotoxic carcinogen1,3-butadiene on chromatin and transcription

city: Chapel Hill

first: Terry

last: Furey

state: North Carolina

address: 5022 Genetic Medicine Bldg, CB#7264

institute: University of North Carolina at Chapel Hill

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Epigenetic effects of environmental chemicals are under intense investigation to fill existing knowledge gaps between environmental/occupational exposures and adverse health outcomes. Chromatin accessibility is one prominent mechanism of epigenetic control of transcription, and understanding of the chemical effects on both could inform the causal role of epigenetic alterations in disease mechanisms. In this study, we hypothesized that baseline variability in chromatin organization and transcription profiles among various tissues and mouse strains influence the outcome of exposure to the DNA damaging chemical 1,3-butadiene. To test this hypothesis, we evaluated DNA damage along with comprehensive quantification of RNA transcripts (RNA-seq), identification of accessible chromatin (ATAC-seq), and characterization of regions with histone modifications associated with active transcription (ChIP-seq for acetylation at histone 3 lysine 27, H3K27ac). We collected these data in the lung, liver and kidney of mice from two genetically divergent strains, C57BL/6J and CAST/EiJ, that were exposed to clean air or to 1,3-butadiene (~600 ppm) for 2 weeks. We found that tissue effects dominate differences in both gene expression and chromatin states, followed by strain effects. At baseline, xenobiotic metabolism was consistently more active in CAST/EiJ, while immune system pathways were more active in C57BL/6J across tissues. Surprisingly, even though all three tissues in both strains harbored butadiene-induced DNA damage, little transcriptional effect of butadiene was observed in liver and kidney. Toxicologically-relevant effects of butadiene in the lung were on the pathways of xenobiotic metabolism and inflammation. We also found that variability in chromatin accessibility across individuals (i.e., strains) only partially explains the variability in transcription. This study showed that variation in the basal states of epigenome and transcriptome may be useful indicators for individuals or tissues susceptible to genotoxic environmental chemicals.

overall_design: Investigation of strain-specific chromatin accessibility, H3k27ac modifications, and gene expression differences in lung, liver, and kidney tissue from CAST/EiJ and C57BL/6J mice, and how the gene regulatory landscape changes in response to 1,3-Butadiene exposure

first: Jennifer

last: Israel

first: Terrence


title: Inhibition of the kinesin spindle protein enhances the activity of pomalidomide and dexamethasone in multiple myeloma

first: Enrique

last: Ocio

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

sample_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: DNA methylation, through DNMT1, has an essential role in the development of gastrointestinal smooth muscle cells and disease [miRNA-Seq]

type: Non-coding RNA profiling by high throughput sequencing


title: Generating a robust prediction model for stage I lung adenocarcinoma recurrence after surgical resection

city: WARREN

first: nien

last: wei

state: NJ

address: 9 northridge way

institute: Auspex Diagnostics

summary: 211 FFPE NSLC surgical samples were used to generate  recurrence prediction models

overall_design: Microarray was used to study gene expression difference to generate prediciton models

first: Nien-chih

last: Wei


title: Inner-ear miRNA Time-course Expression

city: Tucson

first: Dominic

last: LaRoche

state: AZ

address: 3430 E. Global Loop

institute: HTG Molecular Diagnostics

summary: The purpose of the study is to evaluate out whether the pattern of expression over time is similar between cells from the CVG, NC, and OV cell types.

overall_design: Three replicates from cells from three different parts of the inner ear, the vestibulochlear complex, neural crest, and the otic vesicle (CVG, NC, and OV, respectively), are measured over three time points. The unit of measurement for the time points 1, 2, and 3 are the developmental stages 13, 14, and 15 respectively.

first: Akihiro

last: Matsuoka

first: Bonnie

last: LaFleur


title: DNA methylation, through DNMT1, has an essential role in the development of gastrointestinal smooth muscle cells and disease


title: KMT2D regulates p63 target enhancers to coordinate epithelial homeostasis

status: Public on Feb 12 2018

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania


title: Single cell transcriptomic analysis (InDrops) of mouse FoxP3- CD4+ Tconv cells and FoxP3+ regulatory CD4+ T cells isolated from spleen and colon [MouseTreg_ColonSpleenSPFGF]

first: CBDM

last: Lab

first: David

last: Zemmour

first: Christophe

last: Benoist


title: DNA methylation, through DNMT1, has an essential role in the development of gastrointestinal smooth muscle cells and disease [RNA-Seq]

first: Seungil

last: Ro

first: Brian

last: Jorgensen

first: Robyn

last: Berent

first: Se


title: KMT2D regulates p63 target enhancers to coordinate epithelial homeostasis [RNA-Seq]

summary: KMT2D plays a critical role in the control of epithelial enhancers and p63 target gene expression, including the re-quirement of KMT2D for the maintenance of epithelial progenitor gene expression and the coordination of proper terminal differentiation.

overall_design: Determination of gene expression changes in keratinocytes with depletion of KMT2D by shRNA (shKMT2D)

last: Lin-Shiao

last: Capell


title: Single cell transcriptomic analysis (InDrops) of mouse FoxP3+ regulatory CD4+ T cells isolated from spleen and colon


title: Gene expression profiling signatures allow the identification of unclassifiable leukemic B-cell lymphoid neoplasms

city: Barcelona

first: Guillem

last: Clot

address: Rosselló, 153

institute: IDIBAPS

summary:
Gene expression analysis of different B-cell chronic lymphoproliferative disorders
We performed gene expression profiling to develop a robust GEP-molecular classifier for leukemic B-CLPD

overall_design: A total number of 189 purified leukemic B-CLPD samples (including: CLL (n=54), FL (n=12), HCL (n=4), HCLv (n=4), LPL (n=6), cMCL (n=30), nnMCL (n=24), SDRPL (n=4), SMZL (n=23), and B-CLPD NOS (n=28))were processed with Affymetrix U133 Plus2.0 array.

first: Alba

last: Navarro

first: Sílvia

last: Beà


title: Genome-wide mapping of SRC-3 binding in the liver at CT4.

city: Houston

first: Bokai

last: Zhu

state: Texas

address: One Baylor Plaza, M813

department: MCB

institute: Baylor College of Medicine

summary: We reported the cistrome of steroid receptor co-activator SRC-3 in the liver at CT4

overall_design: Examination of SRC-3 binding at CT4 in liver

first: Bert

last: O'Malley


title: Differential Argonaute-2 RNA immunoprecipitation of control cells versus cells overexpressing miR-146a followed by deep sequencing (Ago2 RIP-seq)

city: Lisbon

first: Francisco

middle: J.

last: Enguita

address: Av. Professor Egas Moniz

department: Instituto de Medicina Molecular

country: Portugal

institute: Faculdade de Medicina, Universidade de Lisboa

summary: We undertook an unbiased approach based on differential Argonaute-2 (Ago2) RNA immunoprecipitation followed by deep sequencing (Ago2 RIP-seq) to unravel the molecular mechanism(s) underlying miR-146a function, namely the relevant mRNA target(s). Ago2 is a crucial protein that engages with both miRNA and its mRNA target(s) in the RISC complex. To overcome the problem of lack of commercially available high affinity antibodies against Ago2, we took advantage of a genetically modified mouse in which endogenous Ago2 is replaced with a N-terminal tagged version of the protein (3xFLAG- 6xHIS), thus allowing stringent purification (i.e., with low unspecific background) of the RNA molecules bound to Ago2 (upon UV-crosslinking), followed by RNA-sequencing. In order to enrich for miR-146a targets, we transduced purified CD3+ T cells (we could not use γδ T cells due to insufficient cell numbers for this approach) with a miR-146a-expressing retrovirus (with~12-fold overexpression of miR-146a). We thereby identified 225 putative mRNAs after differential Ago2-RIP-seq, from which 96 (42,7%) had a predicted miR-146a binding site in their 3’ UTR region.

overall_design: Identification of miR-146a targets in CD3+T lymphocytes based on its differential overexpression

first: Nina

last: Schmolka

first: Pedro

middle: H

last: Papotto

first: Paula

last: Vargas Romero

first: Tiago

last: Amado

middle: J

first: Ana

last: Amorim

middle: F

last: Rodrigues

first: Katrina

last: Gordon

first: Mark

last: Boldin

first: Karine

last: Serre

first: Amy

last: Buck

first: Anita

middle: Q

last: Gomes

first: Bruno

last: Silva-Santos


title: Inhibition of the kinesin spindle protein enhances the activity of pomalidomide and dexamethasone in multiple myeloma [In Vivo]

first: Enrique

last: Ocio

first: Susana

last: Hernández-García

first: Laura

last: San-Segundo

first: Lorena

last: González-Méndez

first: Luis

last: Corchete

first: Irena

last: Misiewicz-Krzeminska

first: Montserrat

last: Martín-Sánchez

first: Ana-Alicia

last: López-Iglesias

first: Esperanza

middle: M

last: Algarín

first: Teresa

last: Paíno

first: Brian

last: Tunquist

first: María-Victoria

last: Mateos

first: Norma

last: Gutiérrez

first: Elena

last: Díaz-Rodriguez

first: Mercedes

last: Garayoa


title: PP2A mediates malignant pre-B cell survival through Lineage-Specific control of cellular redox homeostasis

city: San Francisco

first: Huimin

last: Geng

state: CA

address: 513 Parnassus Ave., MSB HSW 1201

department: Department of Laboratory Medicine

institute: UCSF

summary: Ppp2r1afl/fl mouse bone marrow pre-B cells were transduced with an BCR-ABL1 vector. The BCR-ABL1 transduced Ppp2r1afl/fl pre-B cells were then transduced with an empty vector (EV), or a Cre vector for Cre-mediated PP2A deletion. Effect of PP2A deletion in the BCR-ABL1 pre-B cells were studied by Affymetrix GeneChip Mouse Genome ST1.0 Array

overall_design: BCR-ABL1 transduced Ppp2r1afl/fl mice bone marrow pre-B cells were tranduced with an empty vector (EV) or a Cre vector for PP2A deletion

first: Gang

last: Xiao

first: Markus

last: Muschen


title: Knockdown of FOXP1 promotes the development of lung adenocarcinoma

status: Public on Feb 10 2018

city: Shanghai

first: Yi

last: Xu

state: Shanghai

address: No. 221, West Yanan Road

department: Department of Respiration

institute: The Affiliated HuaDong hospital of Fudan University

summary: Lung cancer is one of the most common cancers in the world, which accounts for about 27% of all cancer deaths. However, the mechanisms underlying the pathogenesis of lung cancer cells remain largely elusive. In this study, we examined the role of the Forkhead box protein P1 (FOXP1) in lung cancer development. Our Oncomine analysis shows that FOXP1 is downregulated in lung adenocarcinoma compared with normal lung tissue. Knockdown of FOXP1 promotes the proliferation growth and invasion of PC9 and A549 cells by regulating genes of chemokine signaling molecules, including CCR1, ADCY5, GNG7, VAV3, and PLCB1. Simultaneous knockdown of CCR1 and FOXP1 attenuated FOXP1 knockdown-induced increase of lung cancer cell growth. Finally, knockdown of FOXP1 in PC9 cells promotes the tumorigenesis via CCR1 signaling in xenograft mouse model. Taken together, our data suggest that FOXP1 plays important roles in preventing lung adenocarcinoma development via suppressing chemokine signaling pathways. Novel strategies might be developed to prevent the development of lung adenocarcinoma by targeting FOXP1

overall_design: Three control and three FOXP1 knockdown A549 cell lines were subjected to RNA sequencing. Total RNA was extracted 48 h after the FOXP1siRNA or control siRNA transfected. With the RNA sequencing data prepared, the expression abundance (FPKM) value of each gene was estimated by running cufflinks and the differential expressed genes were assessed by cuffdiff. Only those genes with |fold change|> 2 and adjusted p value < 0.01 were recognized as statistically differentially expressed between two groups. The adjusted p value was obtained through applying Benjamini and Hochberg's (BH) false discovery rate correction on the original p value, and fold change threshold was selected based on our purpose of focusing on significantly differentially expressed genes.

first: Hua

last: Sheng

first: Xiangyang

last: Li


title: Methylation profiling of preclinical ETMR models

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

type: Methylation profiling by genome tiling array

summary: Methylation profiles of preclinical ETMR models were generated and compared to reference primary human tumors to determine the molecular fidelity of the preclinical model systems.

overall_design: 2 preclinical ETMR models (BT183: tumor, cell line, labeled cell line, orthotopic xenograft; NCH3602: tumor, orthotopic PDX) were profiled using either the Infinium HumanMethylation450 BeadChip (450k) array or the Infinium MethylationEPIC BeadChip (EPIC) array.


title: The protective effect of celastrol in ANIT-induced cholestasis

status: Public on Feb 09 2018

city: 云南

first: Qi

last: Zhao

address: State Key Laboratory of Phytochemistry and Plant Resources in West China, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China

summary:
Purpose: The goals of this study was to (1) evaluate the protective effect of celastrol on alpha-naphthylisothiocyanate (ANIT)-induced cholestasis and (2) which genes were recovered by celastrol.
Methods:To investigate the protective effect of celastrol on ANIT-induced cholestasis, the WT mice were randomly assigned into two groups, respectively (n=3): (1) ANIT; (2) ANIT+Celastrol. ANIT+Celastrol group was orally treated with celastrol (10 mg/kg dissolved in 1% DMSO + 2% Tween 80 + 97% water) for 5 consecutive days. After celastrol was treated for 3 days, ANIT and ANIT+Celastrol groups were given a single oral dose of ANIT. All mice were killed 48 h after ANIT administration. Liver samples were harvested and frozen at -80 °C before analysis.
Results: A total of 978 DEGs were identified. Large numbers of these DEGs were related to activation of SIRT1, which included increased FXR signaling and inhibition of PPARγ, nuclear factor-kappa B (NF-κB), and P53 signaling.
Conclusions: Celastrol could protect ANIT-induced cholestasis by recovering disrupted Sirt1 level.

overall_design: 6 hepatic mRNA profiles  were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Fei


title: YAP transcriptionally regulates ErbB2 to promote liver cell proliferation

city: Vancouver

first: Pamela

last: Hoodless

state: British Columbia

address: 675 West 10th Avenue

department: Terry Fox Laboratories

country: Canada

institute: BC Cancer Agency

summary: The Hippo signaling pathway is implicated in regulation of liver size and dysregulation of this pathway contributes to tumorigenesis. The transcriptional targets and downstream pathways of the Hippo pathway effector YAP that contribute to liver growth have yet to be well-characterized. We examined the liver transcriptome in response to YAP overexpression and identify the ErbB signaling pathway as a mediator of cell growth downstream of YAP. ErbB2 is transcriptionally regulated by YAP in both the mouse liver and in HepG2 human hepatoma cells. Knockdown of YAP or pharmacological inhibition with verteporfin reduced ERBB2 levels in HepG2 cells. Analysis of ChIP-seq data revealed enrichment of the transcription factor TEAD4 at the ERBB2 promoter. Using luciferase reporter and chromatin immunoprecipitation assays, we show that YAP and TEAD directly bind to and activate a regulatory element in the ErbB2 promoter in both the mouse liver and HepG2 cells. Functionally, knockdown of YAP reduced EGF-induced ERBB2-mediated HepG2 cell proliferation and PI3K/AKT activation. Our findings highlight a mechanism by which YAP exerts its effects on liver cell proliferation through the ErbB signaling pathway by directly regulating the transcription of ErbB2.

overall_design: mRNA expression profiling of YAP overexpression (+DOX) and control (-DOX) mouse livers in triplicate.

first: Evan

middle: Y

last: Wang


title: Single cell RNA-seq reveals heterogeneity and hierarchy of mouse mammary epithelia

city: Macau

first: Heng

last: Sun

address: Avendia da Universidade, Taipa

department: Faculty of Health Sciences

country: Macau

institute: University of Macau

summary: The mammary epithelia are mainly composed of two distinct lineages, the basal and luminal cells. Due to the limitation of traditional transcriptome analysis of bulk mammary cells, the hierarchy and heterogeneity of mammary cells within these two lineages remain unclear. Hence, we have performed single cell RNA-seq on mammary epithelial cells of virgin and pregnant mice. Based on the respective gene expression profiles, we found mammary cells are highly heterogeneous and can be classified into distinct subgroups with signature markers. Besides, we identified and verified a rare CDH5+ subpopulation of basal lineage as quiescent mammary gland stem cells (MaSCs). Furthermore, knockout of Cdh5 in mouse mammary cells via CRISPR-Cas9 significantly impairs cell stemness and promotes the cell differentiation to luminal lineage. In addition, via pseudo-temporal analysis, we reconstructed the mammary epithelia developmental trajectory and revealed the relevant changes of gene expression and biological functions of mammary cells along the developmental process.

overall_design: Basal and luminal cells form mammary glands of virgin or pregnant (at day 12) FVB mice were FACS-purified for single cell RNA-seq.

first: Chuxia

last: Deng


title: Expression data from HCV infected hepatoma carcinoma cell line Huh7-MAVSR cells

status: Public on Feb 08 2018

first: Yanan

address: Yueyang Road 320

institute: Institut Pasteur of Shanghai  Chinese Academy of Science

summary: Hepatitis C virus (HCV) infection is a major cause of chronic hepatitis, liver cirrhosis and hepatocellular carcinoma. HCV can be sensed by host innate immunity to induce expression of interferons (IFNs) and a number of antiviral effectors. HCV-encoded NS3/4 serine protease can subvert host innate immune responses by cleaving MAVS, a critical adaptor protein in the RLR-mediated IFN signaling. To study innate immunity in the context of HCV infection, we constructed Huh7-MAVSR cells which express a mutant MAVS resistant to NS3/4A cleavage. HCV infection induces robust IFN response in Huh7-MAVSR cells, providing a cellular system to study antiviral innate immune response against HCV infection. To analyze host innate antiviral effectors against HCV infection, we performed an mRNA microarray analysis in the HCV-infected Huh7-MAVSR cells.

overall_design: Huh7-MAVSR cell were infected with HCVcc at an MOI of 5 for 12, 24, 48, 72 hours. The uninfected Huh7-MAVSR cells that are similarly cultured for 72 h were used as a mock infection control. The totoal cellular RNAs were extracted and analyzed by an mRNA microarray analysis for determining genes that are differentially expressed in the HCV-infected cells.

first: Jin

last: Zhong

first: Xuezhi

last: Cao


title: Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes [RNA-seq]

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

department: IT Division

country: Norway

institute: University of Bergen

summary: The NF-κB transcription factors are activated via diverse molecular mechanisms in response to various types of stimuli. A plethora of functions associated with specific sets of target genes could be regulated differentially by this factor, affecting cellular response to stress including an anticancer treatment. Here we aimed to compare subsets of NF-κB-dependent genes induced in cells stimulated with a pro-inflammatory cytokine and in cells damaged by a high dose of ionizing radiation (4 and 10 Gy). The RelA-containing NF-κB species were activated by the canonical TNFα-induced and the atypical radiation-induced pathways in human osteosarcoma cells. NF-κB-dependent genes were identified using the gene expression profiling (by RNA-Seq) in cells with downregulated RELA combined with the global profiling of RelA binding sites (by ChIP-Seq), with subsequent validation of selected candidates by quantitative PCR. There were 37 NF-κB-dependent protein-coding genes identified: in all cases RelA bound in their regulatory regions upon activation while downregulation of RELA suppressed their stimulus-induced upregulation, which apparently indicated the positive regulation mode. This set of genes included a few “novel” NF-κB-dependent species. Moreover, the evidence for possible negative regulation of ATF3 gene by NF-κB was collected. The kinetics of the NF-κB activation was slower in cells exposed to radiation than in cytokine-stimulated ones. However, subsets of NF-κB-dependent genes upregulated by both types of stimuli were essentially the same. Hence, one should expect that similar cellular processes resulting from activation of the NF-κB pathway could be induced in cells responding to pro-inflammatory cytokines and in cells where so-called “damage-induced inflammation” response was initiated by ionizing radiation

overall_design: We sequenced mRNA from wild type U2OS cells and cells transiently transfected using siRNA specific for RELA gene or control siRNA. Cells were untreated (control) or stimulated using TNFalpha cytokine for specific time or subjected to ionizing radiation with subsequent recovery. Three biological replicates were performed and sequenced.

first: Patryk

last: Janus

first: Katarzyna

last: Szołtysek

first: Piotr

last: Widłak


title: Treg cells limit IFN-g production to control macrophage accrual and phenotype during skeletal muscle regeneration

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: We report transcriptional characterization of skeletal muscle macrophage subsets in normal and injured muscle after intramuscular injection with cardiotoxin. We profiled transcriptional differences in macrophage subsets from mice depleted of Treg cells using Foxp3-DTR mice. We uncovered an IFN-g-centered regulatory loop, in which Treg cells inhibit NK and T cells to control macrophage accumulation and phenotype during muscle regeneration.

overall_design: Mice were injected with cardiotoxin intramuscularly and muscle macrophage subsets were sorted by FACS directly into TriZol. Gene expression profiling was performed on Affymetrix Mouse Gene 1.0 ST Arrays.

first: Marisella

last: Panduro

first: Diane

last: Mathis

first: Christophe

last: Benoist


title: Gene expression profiling of GSK3 inhibitor (CHIR99021)-treated intestinal organoids

city: Kyoto

first: Masamichi

last: Imajo

address: Yoshidakonoe-cho, Sakyo-ku,

country: Japan

institute: Kyoto University

summary: Acting downstream of many growth factors, extracellular signal-regulated kinase (ERK) plays a pivotal role in regulating cell proliferation and tumorigenesis, where its spatiotemporal dynamics, as well as its strength, determine cellular responses. Here, we uncover the ERK activity dynamics in intestinal epithelial cells (IECs) and their association with tumour characteristics. In vivo imaging identified two distinct modes of ERK activity, sustained and pulse-like activity, in IECs. The sustained and pulse-like activity depended on ErbB2 and EGFR, respectively. Notably, deregulated activation of Wnt signalling, the earliest event in intestinal tumorigenesis, augmented EGFR signalling and exalted it to a dominant driver of ERK activity dynamics, which rendered IECs addicted to EGFR signalling. Furthermore, the frequency of ERK activity pulses was also increased to promote cell proliferation. Thus, ERK activity dynamics are defined by composite inputs from EGFR and ErbB2 signalling in IECs and their alterations underlie tumour-specific sensitivity to pharmacological EGFR inhibition.  In this microarray analysis, we aimed to elucidate molecular mechanisms that mediate Wnt signalling activation-induced alterations in EGFR-ERK signalling dynamics.

overall_design: For microarray analysis, we performed two independent series of experiments. Total RNA was extracted from intestinal organoids cultured in the ENR media supplemented with or without CHIR99021 (5 microM) for four days as described above. Synthesis of cDNA, in vitro transcription and labelling of cRNA, and hybridization to the Mouse Gene 1.0 ST arrays (Affymetrix, Santa Clara, CA, USA) were performed according to the manufactures’ protocols. The CEL files were analyzed by Transcriptome Analysis Console (TAC) 4.0 software (Thermo Fisher Scientific). Expression signals of all genes (probe sets) were calculated using the RMA algorithm.

first: Yu

last: Muta

first: Atsuro

last: Sakurai

first: Michiyuki

last: Matsuda


title: Next Generation Sequencing Provides Transcriptional Analysis for Estradiol Effects in Skeletally Immature (7-weeks old) Female WT and Estrogen Receptor Alpha Knockout Mice

city: New York

first: Sunil

last: Wadhwa

address: 630 West 168th Street

institute: Columbia University

summary: Temporomandibular joint degenerative disease (TMJ-DD) is a chronic form of TMJ disorder that specifically afflicts people over the age of 40 and targets women at a higher rate than men. Prevalence of TMJ-DD in this population suggests that estrogen loss plays a role in the disease pathogenesis. Thus, the goal of the present study was to determine the role of estrogen on chondrogenesis and homeostasis via estrogen receptor alpha (ERα) during growth and maturity of the joint. Young and mature WT and ERαKO female mice were subjected to ovariectomy procedures and then given placebo or estradiol treatment. The effect of estrogen via ERα on fibrocartilage morphology, matrix production, and protease activity was assessed. In the young mice, estrogen via ERα promoted mandibular condylar fibrocartilage chondrogenesis partly by inhibiting the canonical Wnt signaling pathway through upregulation of sclerostin (Sost). In the mature mice, protease activity was partly inhibited with estrogen treatment via the upregulation and activity of protease inhibitor 15 (Pi15) and alpha-2-macroglobulin (A2m). The results from this work provide a mechanistic understanding of estradiol on TMJ growth and homeostasis and can be utilized for development of therapeutic targets to promote regeneration and inhibit degeneration of the mandibular condylar fibrocartilage.

overall_design: Examination and comparison of the role of 17β-estradiol (E2) via estrogen receptor alpha (Eralpha) on the transcriptional regulation of genes in the mandibular condylar fibrocartialge of skeletally immature (7-week old) female mice.

first: Jennifer

last: Robinson


title: Expression data of e13.5 Sox-GFP forming digit, e14.5 Lgr5-GFP+ interzone and e14.5 GFP- surrounding tissues in digit

city: Hong Kong S.A.R.

first: Kathryn

last: Cheah

state: Hong Kong

address: 3/F, Laboratory Block, 21 Sassoon Road, Pokfulam, Hong Kong

department: School of Biomedical Sciences

institute: University of Hong Kong

summary: Lgr5 is a novel marker expressing in the interzone from around e14.5 of developing synovial joint. By comparing the expression profiles of e14.5 Lgr5+ interzone cells, surrounding Lgr5- non-interzone cells and also e13.5 digit, we have identified some differential expressing genes in the interzone. We have generated bulk RNAseq data of e14.5 Lgr5+ interzone cells, surrounding non-interzone cells and e13.5 Sox9+ chondrocytes cells in digit.

overall_design: Sox9+ and Lgr5+ cells were isolated from e13.5 Sox9-eGFP and e14.5 Lgr5-GFP-CreERT mice, respectively, GFP+ve and -ve cells were sorted and collected with FACSAria I flow cytometer. Total RNA was extracted from the collected cells with mirVana™ miRNA Isolation Kit (Ambion) according to the manufacturer’s protocol. cDNA libraries were constructed with 10ng of RNA using SMARTer Ultra Low Input RNA Kit for Sequencing (v3, Illumina) and DNA sequencing performed using the Illumina HiSeq platform.

first: Chan

middle: C

last: Wilson

first: Ben

last: Niu


title: USP15-dependent lysosomal pathway controls p53-R175H turnover in ovarian cancer cells

status: Public on Feb 07 2018

first: Achuth

last: Padmanabhan

state: TX

address: BCM-Michael DeBakey Center Room: BCMM-M527 Mail Stop: BCM130

department: Molecular and Cellular Biology

summary: Gain-of-function p53 mutants such as p53-R175H form stable aggregates that accumulate in cells and play an important role in cancer progression. Selective degradation of gain-of-function p53 mutants has emerged as a highly attractive therapeutic strategy to target cancer cells harboring specific p53 mutations. We identified a small molecule called MCB-613 to cause rapid ubiquitination, nuclear export, and degradation of p53-R175H through lysosome-mediated pathway leading to catastrophic cancer cell death. In contrast to its effect on the p53-R175H mutant, MCB-613 causes slight stabilization of p53-WT and has weaker effects on other p53 gain-of-function mutants. Using state-of-the-art genetic and chemical approaches, we identified the deubiquitinase USP15 as the mediator of MCB-613’s effect on p53-R175H and established USP15 as a selective upstream regulator of p53-R175H in ovarian cancer cells. These results confirm that distinct pathways regulate the turnover of p53-WT and the different p53 mutants and open new opportunities to selectively target them.

overall_design: Comparison between the RNAseq data between NSC632839 (a deubiquitinase inhibitor) treated and MCB613 treated MCF7 breast cancer cell

first: Nicholes

last: Candelaria

first: Kwong-Kwok

last: Wong

first: Bryan

last: Nikolai

first: David

last: Lonard

first: Bert

middle: W

last: O'Malley

first: JoAnne

last: Richards


title: Estrogen Promotes Mandibular Condylar Fibrocartilage Chondrogenesis and Inhibits Degeneration Via Estrogen Receptor Alpha in Female Mice

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

overall_design: Refer to individual Series


title: PRDM9 methyltransferase is essential for meiotic DSB formation

city: Montpellier cedex 5

first: Julie

middle: A. J.

last: Clement

address: 141, rue de la Cardonille

department: IGH

country: France

institute: CNRS

summary: The programmed formation of hundreds DNA double strand breaks (DSBs) is essential for proper meiosis and fertility. In mice and humans, the location of these breaks is determined by the meiosis-specific protein PRDM9, through the DNA binding specificity of its zinc finger domain. PRDM9 also has methyltransferase activity. Here, we show that this activity is required for H3K4me3 and H3K36me3 deposition and for DSB formation at PRDM9 binding sites. By analyzing mice that express two PRDM9 variants with distinct DNA binding specificities, we reveal severalthe basic principles of PRDM9-dependent DSB site determination, in which an excess of sites are designated through PRDM9 binding and subsequent histone methylation, from which a subset are selected for DSB formation.

overall_design: H3K4me3-, DMC1-ChIPseq experiments were performed on testis from different mouse lines

first: Boubou

last: Diagouraga

middle: A

last: Clément

first: Laurent

last: Duret

first: Jan

last: Kadlec

first: Bernard

last: de Massy

first: Frédéric

last: Baudat


title: CLIP analysis of AEG1

city: Durham

last: Reid

state: NC

address: 436 Nanaline Duke Bldg., Box 3709 DUMC

department: Biochemistry

institute: Duke University

summary: Includes HITS-CLIP and PAR-CLIP of AEG1, including negative controls

overall_design: AEG-1 bound RNA profiles examinated by HITS-CLIP and PAR-CLIP,  coupled with deep sequencing, in duplicate for HITS-CLIP, using Illumina HiSeq.

first: Jack

last: Hsu


title: Sequential enhancer sequestration dysregulates recombination center formation at the IgH locus

city: Baltimore

first: Xiang

last: Qiu

address: 251 Bayview Blvd.

institute: National Institutes of Health

summary: We reoprt that  transcriptional level of distal VH is dependent of both intronic enhancer (Eµ) and intergenic control region 1 (IGCR1).

overall_design: Examination of total RNA from different Pro-B cell lines.

first: Gita

last: Kumari

first: Tatiana

last: Gerasimova

first: Hansen

last: Du

first: Lawal

last: Labaran

first: Amit

last: Singh

first: Supriyo

last: De

first: William

last: Wood III

first: Kevin

last: Becker

first: Weiqiang

last: Zhou

first: Hongkai

last: Ji

first: Ranjan

last: Sen


title: RNA-seq of shEZH2 cells

city: Providence

first: Nicola

last: Neretti

state: RI

address: 70 Ship St

department: Department of Molecular Biology, Cell Biology & Biochemistry

institute: Brown University

summary: Downregulation of EZH2 Leads to Cellular Senescence with Features of SASP

overall_design: Cells were infected with a lentivirus vector expressing shRNA against EZH2 and harvested at 4 and 8 days after infection. Total RNA was harvested from cells using Trizol reagent (Invitrogen) and further purified using the Purelink RNA Mini kit (Invitrogen) with DNase I digestion. RNA library preparation with polyA selection and Illumina HiSeq 2x150bp sequencing was performed by GeneWiz Inc. Paired-end reads were quality trimmed using Trim galore v0.4.0 and subsequently aligned to the human reference genome, hg19, using HISAT2 v2.1.0. Reads mapping to annotated genes were quantified using featureCounts (Liao et al., 2014). Differential gene expression was determined using DESeq2 v1.12.4 (Love et al., 2014) and significance was defined as FDR-corrected p-values of <0.05. The log2 fold change for each gene was used to rank the list of genes for GSEAPreranked analysis (Subramanian et al., 2005). FPKM values were calculated using DESeq2 and Z‐scores were generated from FPKMs

first: Ito

last: Takahiro

first: Sedivy

last: John


title: Transcriptomic analysis of multiple myeloma cell lines

status: Public on Feb 06 2018

city: Muraoka-Higashi 2-chome Fujisawa

first: Kazuhide

last: Nakayama

state: Kanagawa

department: Regenerative medicine Unit

institute: Takeda Pharmaceutical Company Limited

summary: We found that a small molecule inhibitor of PRMT4 inhibited cell growth of a subset of multiple myeloma cell lines. To identify biomarkers that predict the sensitivity of myeloma cells to PRMT4 inhibition, we performed transcriptomic analysis of multiple myeloma cell lines.

overall_design: Amplicon sequencing of thirteen multiple myeloma cell lines was performed on the Ion Torrent platform. Steady-state gene expression profile of sensitive cells were compaired with that of insensitive cells.

first: Atsushi

last: Kiba

first: Yuji

last: Baba

first: Kuniko

last: Kikuchi

first: Hirokazu

last: Tozaki


title: IL-10 induces a STAT3-dependent autoregulatory loop in Th2 cells that promotes Blimp-1 restriction of cell expansion via antagonism of STAT5 target genes

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

institute: University of Pittsburgh

summary: Blimp-1 expression in T cells extinguishes the T follicular helper cell fate and drives terminal differentiation, but also limits autoimmunity. Although various factors have been described to control Blimp-1 expression in T cells, little is known about what regulates Blimp-1 expression in Th2 cells and the molecular basis of its actions. Herein, we report that STAT3 unexpectedly played a critical role in regulating Blimp-1 in Th2 cells. Furthermore, we found that the cytokine IL-10 acted directly on Th2 cells and was necessary and sufficient to induce optimal Blimp-1 expression through STAT3. Together, Blimp-1 and STAT3 amplified IL-10 production in Th2 cells, creating a strong autoregulatory loop that enhanced Blimp-1 expression. Increased Blimp-1 in T cells antagonized STAT5-regulated cell cycle and anti-apoptotic genes to limit cell expansion. These data elucidate the signals required for Blimp-1 expression in Th2 cells and reveal an unexpected mechanism of action of IL-10 in T cells, providing insights into the molecular underpinning by which Blimp-1 constrains T cell expansion to limit autoimmunity.

overall_design: RNAseq of activated undifferentiated CD4 T cells with or without exogenous expression of Blimp-1.

first: Dragana

last: Jankovic

first: Alejandro

middle: V

last: Villarino

first: Franziska

last: Petermann

first: Angela

last: Hettinga

first: Dror

last: Shouval

first: Scott

middle: B

last: Snapper

first: Susan

last: Kaech

first: Stephen

middle: R

last: Brooks

first: Golnaz

last: Vahedi

first: Alan

last: Sher

first: Yuka

last: Kanno

first: John

last: O'Shea


title: KMT2D regulates p63 target enhancers to coordinate epithelial homeostasis [ChIP-Seq]

city: Philadelphia

first: Yemin

last: Lan

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: KMT2D plays a critical role in the control of epithelial enhancers and p63 target gene expression, including the re-quirement of KMT2D for the maintenance of epithelial progenitor gene expression and the coordination of proper terminal differentiation.

overall_design: Characterization of KMT2D, p63 and several histone modifications' occupancy by ChIP-Seq in shRNA KO cell cultures.

first: Enrique

last: Lin-Shiao

first: Brian

last: Capell


title: Rescue of Fragile X syndrome neurons by DNA methylation editing of the FMR1 gene [methylation]

city: CAMBRIDGE

first: Shawn

last: Liu

state: MA

address: 455 MAIN STREET

institute: Whitehead Institute for Biomedical Research

summary: Fragile X syndrome (FXS), the most common genetic form of intellectual disability in male, is caused by silencing of the FMR1 gene by hypermethylation of the CGG expansion mutation in the 5’UTR region of FMR1 in FXS patients. Here, we applied recently developed DNA methylation editing tools to reverse this hypermethylation event. Targeted demethylation of the CGG expansion by dCas9-Tet1/sgRNA switched the heterochromatin status of the upstream FMR1 promoter to an active chromatin state restoring a persistent expression of FMR1 in FXS iPSCs. Neurons derived from methylation edited FXS iPSCs rescued the electrophysiological abnormalities and restored a wild-type phenotype upon the mutant neurons. FMR1 expression in edited neurons was maintained in vivo after engrafting into the mouse brain. Finally, demethylation of the CGG repeats in post-mitotic FXS neurons also reactivated FMR1. Our data establish demethylation of the CGG expansion is sufficient for FMR1 reactivation, suggesting potential therapeutic strategies for FXS.

overall_design: Targeted demethylation of the CGG repeats by dCas9-Tet1/sgRNA reactivates FMR1 in FXS iPSCs and neurons.

first: X

middle: S


title: Epigenetic profiling of children with respiratory allergy

city: Antwerp (Wilrijk)

first: Ken

last: Declerck

address: Universiteitsplein 1

country: Belgium

institute: University of Antwerp

summary: The prevalence of respiratory allergy in children is increasing. Epigenetic changes (e.g. DNA methylation) are plausible underlying molecular mechanisms. Longitudinal birth cohorts are instrumental to study the relation between early-life environmental factors and the development of complex diseases. Our AXA Research Fund and Cefic-LRI supported project explores the hypothesis that chemical exposures during pregnancy can influence the immune system and development of allergy in children. Questionnaire data, as well as cord blood, plus blood and saliva samples at age 11 years, were collected in substudies of two longitudinal birth cohorts in Belgium (FLEHS1 & FLEHS2) and analyzed with  Illumina Methylation 450K BeadChips as well as gene targeted iPLEX MassArrays analysis. The project aims to answer the following questions: 1) can we identify specific changes in epigenetic modifications on DNA from allergic compared to not-allergic children; 2) are these allergy-related epigenetic changes a result of chemical exposure during pregnancy; and 3) did the early life exposures leave an epigenetic “mark” that is maintained through childhood. If chemicals exposures and resulting predictive markers of allergic diseases can be detected early, prevention strategies, particularly in children or before pregnancy, could be developed.

overall_design: Bisulphite converted DNA from 93 cord blood (PBMC fraction), 92 blood (PBMC fraction), 53 saliva samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Sabine

last: Langie

first: Matthieu

last: Moisse

first: Katarzyna

last: Szarc vel Szic

first: Gudrun

last: Koppen

first: Vera

last: Nelen

first: Guy

last: Van Camp

first: Diether

last: Lambrechts

first: Greet

last: Schoeters

first: Wim

last: Vanden Berghe

first: Patrick

last: De Boever


title: Effect of prenatal DHA supplementation on the infant epigenome

city: North Ryde

first: Peter

middle: Laurence

last: Molloy

state: NSW

address: 11 Julis Ave

department: Health and Biosecurity

country: Australia

institute: CSIRO

summary: Evidence is accumulating that nutritional exposures in utero can influence health outcomes in later life. Animal studies and human epidemiological studies have implicated epigenetic modifications as playing a key role in this process, but there are limited data from large well-controlled human intervention trials. This study utilised a large double-blind randomized placebo-controlled trial to test whether a defined nutritional exposure in utero, in this case docosahexaenoic acid (DHA), could alter the infant epigenome. Pregnant mothers consumed DHA-rich fish oil (800 mg DHA/d) or placebo supplements from 20 weeks’ gestation to delivery. Blood spots were collected from the children at birth (n=991) and blood leukocytes at 5 years (n=667). Global DNA methylation was measured in all samples and Illumina HumanMethylation450K BeadChip arrays were used for genome-wide methylation profiling in a subset of 369 children at birth and 65 children at 5 years.   There were no differences in global DNA methylation levels between the DHA and control group either at birth or at 5 years, but we identified 21 differentially methylated regions (DMRs) at birth, showing small DNA methylation differences (<5%) between the treatment groups, some of which seemed to persist until 5 years. The number of DMRs at birth was greater in males (127 DMRs) and in females (72 DMRs) separately, indicating a gender-specific effect.   In conclusion, maternal DHA supplementation during the second half of pregnancy had small effects on DNA methylation of infants. While the potential functional significance of these changes remains to be determined, these findings further support the role of epigenetic modifications in developmental programming in humans, and points the way for future studies.

overall_design: Double-blind randomized placebo-controlled trial in which pregnant mothers consumed DHA-rich fish oil (800 mg DHA/d) or placebo supplements from 20 weeks’ gestation to delivery. Blood spots were collected from the children at birth and blood leukocytes at 5 years. Illumina HumanMethylation450K BeadChip arrays were used for genome-wide methylation profiling in a subset of 369 children at birth and 65 children at 5 years.  This series contains only the neonatal blood spot samples.

first: Susan

last: van Dijk

first: Jing

last: Zhou

first: Timothy

last: Peters

first: Michael

last: Buckley

first: Brodie

last: Sutcliffe

first: Yalchin

last: Oytam

first: Robert

last: Gibson

first: Andrew

last: McPhee

first: Lisa

middle: N

last: Yelland

first: Maria

last: Makrides

middle: L

first: Beverly

last: Muhlhausler


title: Genetic determinants and epigenetic effects of pioneer factor binding [WGBS]

city: Cambridge

first: Sudhir

last: Thakurela

address: 7 Divinity Avenue

institute: HSCRB

summary: Transcription factors (TFs) are the core drivers of gene regulatory networks that control developmental transitions and a complete understanding of how they access, alter and maintain specific gene expression patterns remains an important goal. To begin a systematic dissection of the molecular components that either enable or constrain TF activity, we investigated the genomic occupancy of two distinct TFs, the pioneer factor FOXA2 and the pluripotency-associated factor OCT4 (POU5F1), in both endogenous and ectopic settings. We find that, while stable binding of FOXA2 is highly cell type specific and similar to what is observed for most TFs including OCT4, pioneer activity can be distinguished by notable sampling of additional loci that are occupied in alternative lineages. In our ectopic system, FOXA2 binding can be selectively stabilized at previously sampled sites by co-expressing the lineage specific regulator GATA4. Alternatively, we observe minimal influence of chromatin state on discrete, stabilized binding choices for FOXA2 but a strong bias towards open chromatin for ectopic OCT4 targets. Finally, we demonstrate that FOXA2 binding and nucleosome remodeling at silent loci can occur when the cell cycle is halted in G1, but surprisingly subsequent changes in DNA methylation require DNA replication. Taken together, our results provide several new molecular insights that contribute to our basic understanding of gene regulation and pave the way for a more rational use of ectopic TFs for cellular reprogramming.

overall_design: Ectopic expression of TFs coupled with ChIPseq, WGBS, ChIPBSseq and ATACseq

first: J

last: Donaghey

first: S

first: A

last: Meissner


title: Gene expression of human peripheral blood granulocytes (neutrophils)

status: Public on Feb 05 2018

city: Bethesda

first: WeiPing

last: Chen

state: MD

address: Bldg 8, Room 1A11, NIDDK/NIH

department: GCL

institute: NIDDK/NIH

summary: Goal was to compare if there were gene expression difference at baseline, without treatment, in the neutrophils of individuals with benign neutropenia vs individuals with normal neutrophil counts

overall_design: 7 individuals with neutrophil counts <1500(ANC-L), 5 individuals with neutrophil counts >4000(ANC-H); extreme phenotype design

first: matt

middle: h

last: hsieh

first: griffin

middle: p

last: rodgers


title: Paupar long non-coding RNA promotes KAP1 dependent chromatin changes and regulates olfactory bulb neurogenesis

status: Public on Feb 02 2018

city: Bath

first: Keith

last: Vance

address: Claverton Down

department: Department of Biology and Biochemistry

institute: University of Bath


title: Paupar long non-coding RNA promotes KAP1 dependent chromatin changes and regulates olfactory bulb neurogenesis [CHIP-seq]

summary: These data show that Paupar, a CNS expressed long non-coding RNA (lncRNA), directly and functionally associates with KAP1, an essential epigenetic regulatory protein. Transcriptome profiling of N2A cells identified 1,913 differentially expressed genes whose expression significantly changed (at a 5% false discovery rate [FDR]) greater than 1.4-fold (log2 fold change ≈ 0.5) upon KAP1 depletion. Examination of the intersection of KAP1 and Paupar transcriptional targets showed that Paupar and KAP1 control expression of a shared set of target genes that are enriched for regulators of neuronal function and cell cycle in N2A cells. Furthermore, CHART-seq and ChIP-seq derived Paupar-KAP1 genome-wide co-occupancy maps revealed a 4-fold enrichment of overlap between Paupar and KAP1 bound sequences on chromatin.  This study also indicates that Paupar promotes KAP1 chromatin occupancy and H3K9me3 deposition at a subset of distal targets, through formation of a ribonucleoprotein complex containing Paupar, KAP1 and the PAX6 transcription factor. These observations provide important conceptual insights into the trans-acting modes of lncRNA-mediated epigenetic regulation and the mechanisms of KAP1 genomic recruitment.

overall_design: ChIP-seq analysis of KAP1 chromatin occupancy and microarray profiling of KAP1 target genes in N2A cells

first: Ioanna

last: Pavlaki

first: Farah

last: Alammari

first: Bin

last: Sun

first: Neil

last: Clark

first: Tamara

last: Sirey

first: Sheena

last: Lee

first: Dan

middle: J

last: Woodcock

first: Chris

middle: P

last: Ponting

first: Francis

middle: G

last: Szele


title: Single-cell transcriptomics of the developing lateral geniculate nucleus reveals insights into circuit assembly and refinement

city: Boston

first: Brian

last: Kalish

address: 220 Longwood Ave

department: Neurobiology

institute: Boston Children's Hospital

summary: Coordinated changes in gene expression underlie the early patterning and cell type specification of the central nervous system. However, much less is known about how such changes contribute to later stages of circuit assembly and refinement. In this study, we employ single-cell RNA-sequencing to develop a detailed, whole-transcriptome resource of gene expression across four time points in the developing dorsal lateral geniculate nucleus, a visual structure in the brain that undergoes a well-characterized program of postnatal circuit development. This approach identifies markers defining the major LGN cell types, including excitatory relay neurons, oligodendrocytes, astrocytes, microglia, and endothelial cells. Most cell types exhibit significant transcriptional changes across development, dynamically expressing genes involved in distinct processes including retinotopic mapping, synaptogenesis, myelination, and synaptic refinement. This transcriptomic resource provides a cellular map of gene expression across several cell types of the LGN, and offers insight into the molecular mechanisms of circuit development in the postnatal brain.

overall_design: Examination of four developmental timepoints, each with four replicates. Raw data files were uploaded to SRA under SRP131204. The 6 multiplexed files were assigned SRA accession numbers SRR6510859, SRR6510864, SRR6510872, SRR6510876, SRR6510868, and SRR6510880.

first: Michael

last: Greenberg


title: Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes

city: Bergen

first: Tomasz

last: Stokowy

address: Nygardsgaten 5

institute: University of Bergen


title: Crosstalk between the RNA methylation and histone binding activities of MePCE regulates P-TEFb activation on chromatin

city: Austin

first: Blerta

last: Xhemalce

address: 2500 Speedway

institute: University of Texas at Austin

summary: The switch of RNAP II from the paused to the productive transcription elongation state is a pivotal regulatory step requiring specific phosphorylations catalyzed by the P-TEFb kinase. Nucleosolic P-TEFb activity is inhibited by its interaction with the ribonuclear protein complex built around the 7SK small nuclear RNA (7SK snRNP). MePCE is the RNA methyltransferase that methylates and stabilizes 7SK in the nucleosol. Here we report that MePCE also binds chromatin through the tail of histone H4 to serve as a P-TEFb activator at specific genes important for cellular identity. Notably, this histone binding abolishes MePCE’s RNA methyltransferase activity towards 7SK, explaining why MePCE-bound P-TEFb on chromatin may not be associated with the full 7SK snRNP and is competent for RNAP II activation. Overall, our results suggest that a crosstalk between the histone binding and RNA methylation activities of MePCE regulates P-TEFb activation on chromatin in a 7SK- and Brd4-independent manner.

overall_design: RNA-Seq was performed in MDA-MB-231 shNC (Negative Control) and shMePCE cells. Concomitantly, ChIP-seq was performed in these same cells with antibodies specifically recognizing RNA Polymerase II phosphorylated at S2 or S5 of its CTD, the N-ter of MePCE, as well as GFP (Negative Control) and H3K4me3 (Positive Control). Because, the ChIP-Seq with the MePCE antibody does not work well for single gene inspection, we performed additional ChIP-seq with the MePCE antibody in HeLa-S3-FlpIn cells.

first: Samantha

last: Shelton

first: Nakul

middle: M

last: Shah

first: Nathan

last: Abell

first: Sravan

last: Devanathan

first: Marvin

last: Mercado


title: Next Generation Sequencing Provides Transcriptional Analysis for Estradiol Effects in Skeletally Mature (17-week old) Female WT and Estrogen Receptor Alpha Knockout Mice

city: New York

first: Sunil

last: Wadhwa

address: 630 West 168th Street

institute: Columbia University

summary: Temporomandibular joint degenerative disease (TMJ-DD) is a chronic form of TMJ disorder that specifically afflicts people over the age of 40 and targets women at a higher rate than men. Prevalence of TMJ-DD in this population suggests that estrogen loss plays a role in the disease pathogenesis. Thus, the goal of the present study was to determine the role of estrogen on chondrogenesis and homeostasis via estrogen receptor alpha (ERα) during growth and maturity of the joint. Young and mature WT and ERαKO female mice were subjected to ovariectomy procedures and then given placebo or estradiol treatment. The effect of estrogen via ERα on fibrocartilage morphology, matrix production, and protease activity was assessed. In the young mice, estrogen via ERα promoted mandibular condylar fibrocartilage chondrogenesis partly by inhibiting the canonical Wnt signaling pathway through upregulation of sclerostin (Sost). In the mature mice, protease activity was partly inhibited with estrogen treatment via the upregulation and activity of protease inhibitor 15 (Pi15) and alpha-2-macroglobulin (A2m). The results from this work provide a mechanistic understanding of estradiol on TMJ growth and homeostasis and can be utilized for development of therapeutic targets to promote regeneration and inhibit degeneration of the mandibular condylar fibrocartilage.

overall_design: Examination and comparison of the role of 17β-estradiol (E2) via estrogen receptor alpha (Eralpha) on the transcriptional regulation of genes in the mandibular condylar fibrocartialge of skeletally mature (17-week old) female mice.

first: Jennifer

last: Robinson


title: A novel CD4 T cell population expanded in SLE blood provides B cell help through IL10 and succinate [ATAC-seq]

city: Farmington

first: Diogo

middle: F

last: Troggian Veiga

state: Connecticut

address: 10 Discovery Drive

institute: The Jackson Laboratory

summary: ATAC-seq analysis of CD4 T cell populations obtained in blood of systemic lupus erythematosus (SLE) patients. The overall goal of this study was to determine chromatin accessibility profiles in Tfh cells and CXCR3+ PD1hi CD4+ T cells obtained from blood of SLE donors.

overall_design: CXCR3+ PD1hi CD4+ T cells and Tfh cells were sorted by flow cytometry and ATAC-seq was performed.

first: Simone

last: Caielli

last: Veiga

first: Bojana

last: Domic

first: Elise

last: Murat

first: Romain

last: Banchereau

first: Zhaohu

last: Xu

first: Manjari

last: Chandra

first: Shruti

last: Athale

first: Cheng-han

last: Chung

first: Lynnette

last: Walters

first: Jeanine

last: Baisch

first: Tracey

last: Wright

first: Marilynn

last: Punaro

first: Duygu

last: Ucar

first: Hideki

last: Ueno

first: Joseph

last: Zhou

first: Jacques

first: Virginia

last: Pascual


title: Epigenetic Signatures of Salivary Gland Inflammation in Sjögren's Syndrome.

city: Berkeley

first: Michael

last: Cole

address: 378 Stanley Hall

institute: UC Berkeley

summary: Genome wide DNA methylation profiling of human labial salivary gland (LSG) biopsy samples obtained from 28 female members of the Sjögren's International Collaborative Clinical Alliance (SICCA) Registry. The Illumina HumanMethylation450 BeadChip platform was used to obtain DNA methylation profiles across more than 450,000 highly informative CpG sites. Samples included 15 non-case glands, and 13 glands from patients with Sjögren's Syndrome.

overall_design: Bisulphite converted DNA from the 31 samples (3 replicates) were hybridised to the Illumina 450K Infinium Methylation BeadChip

first: Hong

last: Quach

first: Diana

first: Alice

last: Baker

first: Kimberly

middle: E

last: Taylor

first: Lisa

last: Barcellos

first: Lindsey

last: Criswell


title: A practical evaluation of alignment algorithms for RNA variant calling analysis

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

summary: We performed RNA-seq with ten pieces of breast cancer (invasive ductal carcinoma; luminal B type) tissue and three pieces of adjacent normal tissue from a single patient. These RNA-seq data were used to evaluate the performance of splice-aware aligners.

overall_design: RNA-seq was performed with 10 pieces of  breast cancer tissue and 3 pieces of adjacent normal tissue obtained from a single patient


title: SUMOylation Regulates Transcription by the Progesterone Receptor A Isoform in a Target Gene Selective Manner

city: los Angeles

first: Hany

middle: A

last: Abdel-Hafiz

state: California

address: 110 N George Burns RD, DRoom 3057

department: Medicine/ Medical Oncology

institute: Cedars-Sinai Medical Center

summary: Luminal breast cancers express estrogen (ER) and progesterone (PR) receptors, and respond to endocrine therapies. However, some ER+PR+ tumors display intrinsic or acquired resistance, possibly related to PR. Two PR isoforms, PR-A and PR-B, regulate distinct gene subsets that may differentially influence tumor fate. A high PR-A:PR-B ratio is associated with poor prognosis and tamoxifen resistance. We speculate that excessive PR-A marks tumors that will relapse early. Here we address mechanisms by which PR-A regulate transcription, focusing on SUMOylation. We use receptor mutants and synthetic promoter/reporters to show that SUMOylation deficiency or the deSUMOylase SENP1 enhance transcription by PR-A, independent of the receptors’ dimerization interface or DNA binding domain. De-SUMOylation exposes the agonist properties of the antiprogestin RU486. Thus, on synthetic promoters, SUMOylation functions as an independent brake on transcription by PR-A. What about PR-A SUMOylation of endogenous human breast cancer genes? To study these, we used gene expression profiling. Surprisingly, PR-A SUMOylation influences progestin target genes differentially, with some upregulated, others downregulated, and others unaffected. Hormone-independent gene regulation is also PR-A SUMOylation dependent. Several SUMOylated genes were analyzed in clinical breast cancer database. In sum, we show that SUMOylation does not simply repress PR-A. Rather, it regulates PR-A activity in a target selective manner including genes associated with poor prognosis, shortened survival, and metastasis.

overall_design: T47D human breast cancer cells stably expressing WT or SUMOylation-deficient PR-AK388R were created by transfection of previously cloned PR-negative T47D-Y cells with expression vectors that encode WT PR-A or PR-AK388R mutant. These cell lines were treated with either vehicle control (ethanol) or 10 nM synthetic progestin R5020 for 24 hrs before total RNA harvest. Thus, the experiment contains three cell lines and two treatments. Total RNA was extracted, cRNA was labeled and hybridized to U133 Plus 2 microarrays.

first: Kate

last: Horwitz


title: Luminal lncRNAs Regulation by ERα-controlled Enhancers in a Ligand-independent Manner in Breast Cancer Cells

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

summary: Estrogen receptor-α (ERα) is a ligand-inducible protein which mediates estrogenic hormones signaling and defines the luminal breast cancer phenotype. Recently, we demonstrated that ERα binds chromatin in absence of ligand (apoERα) regulating transcription of protein-coding genes and several lncRNAs. Noteworthy, apoERα-regulated lncRNAs marginally overlap estrogen-induced transcripts representing a signature of luminal breast cancer genes. DSCAM-AS1 is a paradigmatic example of apoERα activity since its expression is largely unaffected by estrogenic treatment despite an E2-induced increment of ERα binding on its promoter. Analysing H3K27ac ChIP-Seq performed in hormone-deprived MCF-7, we identified a set of Super Enhancers (SEs) occupied by apoERα including one mapped in proximity of DSCAM-AS1. Using ChIP-qPCR, we validated ChIP-Seq signal of apoERα, p300 and CTCF at both DSCAM-AS1 TSS and at its associated SE. Furthermore, analysing MCF-7 ChIA-PET data and performing a 3C experiment, we confirmed a long range chromatin interaction between the SE and the DSCAM-AS1 TSS. Interestingly, CTCF binding downstream to DSCAM-AS1 shows an enrichment in hormone-depleted medium as compared to other experimental conditions, indicating that CTCF demarcates enhancer actions at DSCAM-AS1 locus. The analysis of this lncRNA provides a paradigm of transcriptional regulation of a luminal specific apoERα regulated lncRNA.

overall_design: The RNA-seq datasets were obtained from libraries generated with the TruSeq stranded library preparation kit (Illumina) using as input material poly(A+) RNA depleted of ribosomal RNAs fractions. Pool of 6 libraries (pooled at equimolar concentration) was generated, quantified and run on the HiSeq2000 (Illumina) sequencer in 75 nts paired-end sequencing mode following manufacturer instruction. A total of 6 datasets, with an average depth of 91.5 million paired-end reads, were obtained, composed of triplicates of two MCF-7 culture conditions: i) hormone-deprived cells treated with ESR1 mRNA (siRNA) (48h) or hormone-deprived cells treated with control siRNA (siCTR).

first: Valentina

last: Miano

last: Rosti

first: Eleonora

last: Manitta

first: Jamal

last: Elhasnaoui

first: Giulia

last: Basile

first: Michele

last: De Bortoli


title: A non-catalytic function of SETD1A regulates Cyclin K and the DNA damage response [ChIP-seq]

status: Public on Feb 01 2018

first: Richard

last: Koche

state: New York

institute: Memorial Sloan Kettering Cancer Center

summary: We assessed MLL/SET proteins and found that SETD1A is required for survival of acute myeloid leukemia (AML) cells

overall_design: ChIP-seq of Setd1a/Setd1b shRNA-expressing mouse MLL-AF9 leukemia cells, Setd1a knockout mouse MLL-AF9 leukemia cells, and, Setd1a shRNA-expressing mouse NIH3T3 cells. Setd1aflox/flox;CreER and Setd1a+/+;CreER leukemia cells were analyzed at day 3 post-tamoxifen. shRNA-expressing mouse MLL-AF9 leukemia cells and NIH3T3 cells were analyzed at day 4 post-doxycycline.

first: Takayuki

last: Hoshii

first: Scott

last: Armstrong


title: A non-catalytic function of SETD1A regulates Cyclin K and the DNA damage response

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

overall_design: Refer to individual Series


title: Anti-PD-1/anti-CTLA-4 efficacy in melanoma brain metastases depends on extracranial disease and augmentation of CD8+ T cell trafficking

city: Leeds

first: Mihaela

last: Lorger

address: Beckett street

department: Leeds Institute of Cancer and Pathology

institute: University of Leeds

summary: Intracranial B16 melanoma tumors isolated from C57Bl6 mice were analyzed by mRNAseq. Four experimental groups were analyzed: (1) Mice with intracranial tumors receiving IgG; (2) Mice with intracranial tumors receiving anti-PD-1 plus anti-CTLA-4 therapy; (3) Mice with intracranial plus extracranial tumors receiving IgG; (4) Mice with intracranial plus extracranial tumors receiving anti-PD-1 plus anti-CTLA-4 therapy. Taggart et al., PNAS 2018;

overall_design: mRNAseq profiles of intracranial B16 tumours at day 9 post-cancer cell implantation were generated for 4 different experimental groups (biological triplicates)


title: RNA-seq analysis of aortic heart valves in mice

city: Columbus

first: Emily

last: Nordquist

state: OH

address: 575 Children's Crossroad

department: Department of Cardiovascular Research

institute: Nationwide Children's Hospital

summary: In order to asses differences between expression profiles of postnatal and adult mice, RNA-sequencing was performed on RNA from postnatal day 2 and 4 month old murine aortic valves.

overall_design: 6 samples were analyzed: 3 replicates of the postnatal day 2 timepoint and 3 replicates of the 4 month timepoint. Differential expression was ranked based on false discovery rate (<0.1) and fold change (>2).

first: Joy

last: Lincoln

first: Casey

last: Nagel


title: Gene expression profiling on alveolar epithelial cells from mice intratracheally instilled with or without bleomycin or LPS.

city: Birmingham

first: Huachun

last: Cui

state: Alabama

institute: University of Alabama at Birmingham

summary: We applied next-generation sequencing to investigate the gene expression profiles in mouse alveolar epithelial cells (AECs). We identified a number of differentially regulated genes in the AECs of mice with bleomycin induced pulmonary fibrosis and LPS induced acute lung injury.

overall_design: Total RNAs were isolated from AECs of mice intratracheally instilled with saline, bleomycin for 2 or 4 weeks or LPS for 1 day. The RNAs were subjected to high-throughput sequencing (RNA-seq), using Illumina HiSeq 4000. Gene expression profiles were compared between the saline and treatment groups.

first: Gang

last: Liu


title: Analysis of fatty liver disease development and progression in a combined mouse model of hedgehog signaling attenuation and diet-induced hepatic steatosis

city: BETHESDA

first: abdel

last: Elkahloun

address: 50, SOUTH DRIVE

institute: NHGRI-NIH

summary: Nonalcoholic fatty liver disease (NAFLD) is the most common form of liver disease and a leading cause of liver transplantation in the United Sates. Hedgehog (Hh) signaling has been implicated in liver lipid metabolism and the early stages of NAFLD; however, its precise role remains unclear. We examined the prevalence of NAFLD in patients with overt or microform holoprosencephaly (HPE), a disorder associated with germline mutations disrupting Hh signaling. To test the hypothesis that Hh signaling attenuation predisposes to liver steatosis, we subjected Gli2 heterozygous null (Gli2+/-) mice to two unique dietary models of fatty liver. Compared to the general population, the prevalence of NAFLD was significantly higher in the HPE cohort independent of obesity, especially among younger individuals. Gli2 heterozygosity caused increased weight gain and liver steatosis on a high fat diet, and increased liver steatosis in the absence of weight gain on a methionine and choline deficient diet.  Increased liver steatosis in Gli2+/- mice was associated with decreased expression of pro-fibrotic and pro-inflammatory genes and increased expression of PPAR³, a potent anti-fibrogenic and anti-inflammatory regulator. In addition, tumor suppressors p53 and p16INK4 were found to be downregulated in the Gli2+/- mice. Our results indicate that germline mutations affecting Hh signaling predispose to NAFLD with reduced or absent fibrosis, and might increase the risk of hepatocellular carcinoma.

overall_design: Gli2 heterozygous null and wild-type mice we exposed to control or high-fat diet for 12 weeks. Four animals per group were studied, for a total of 16 animals.

first: Ariel

last: Martinez

first: Abdel

first: Maximilian

last: Muenke


title: Tissue-specific gene expression changes in l(3)mbt mutant ovaries [germline]

city: Paris

first: Remi-Xavier

last: Coux

address: 25 rue du docteur Roux

department: Developmental and Stem Cell Biology dpt

institute: Pasteur Institute

summary: We performed RNAseq on embryos laid by somatically complemented l(3)mbt mutant germline to gain a genome-wide view of tissue-specific gene expression changes in L(3)mbt-depleted germline.

overall_design: Examination of gene expression changes in mutant and control germline.

first: Remi

middle: X

first: Ruth

last: Lehmann


title: Antibody-Mediated Inhibition of MICA/B Shedding Promotes NK Cell-Driven Tumor Immunity

first: Lucas

last: Ferrari de Andrade

address: 1425 Madison Avenue

institute: Ichan School of Medicine at Mount Sinai

summary: MICA and MICB (MICA/B) are expressed by many human cancers due to cellular stress and tag cells for elimination by cytotoxic lymphocytes through NKG2D receptor activation.  However, tumors evade this immune recognition pathway through proteolytic shedding of MICA/B proteins.  We rationally designed antibodies targeting the MICA α3 domain, the site of proteolytic shedding, and found that these antibodies prevented loss of cell surface MICA/B by human cancer cells.  These antibodies inhibited tumor growth in multiple fully immuno-competent mouse models and also reduced human melanoma metastases in a humanized mouse model.  Anti-tumor immunity was mediated mainly by NK cells through activation of NKG2D and CD16 Fc receptors.  This novel approach prevents the loss of important immunostimulatory ligands by human cancers and reactivates antitumor immunity.

platform_organism:
Homo sapiens
Mus musculus

overall_design:
[LFDA] Human NK cells were isolated from a healthy volunteer to ~99% purity. These cells were pre-activated with 1,000 U/ml IL-2 overnight. A375 tumor cells were pre-treated with 10 ug/ml of 7C6-hIgG1 or isotype control (BioXcell BE0096) antibodies for 48 hours. Cells were then washed and NK cells were co-cultured with tumor cells for 6 hours in a 5 : 1 ratio. Subsequently, human NK cells were re-sorted and total RNA isolated with genomic DNA digestion with QIAGEN RNeasy RNA isolation kit (74134).  RNA sequencing libraries were generated using the Kapa mRNAseq kit (KapaBiosystems).
[Single Cell RNA-seq] Lung-infiltrated NK cells from mice inoculated intravenously with B16F10-MICA cells (day 0) and treated with isotype control or MICA antibody clone clone 7C6-mIgG2a on days 1 and 2. Analysis on day 7.

last: de Andrade

first: Deng

last: Pan

first: Kai

middle: W

last: Wucherpfennig

first: Daphne

last: Tsoucas


title: Tissue-specific gene expression changes in l(3)mbt mutant ovaries


title: Paupar long non-coding RNA promotes KAP1 dependent chromatin changes and regulates olfactory bulb neurogenesis [gene expression]

first: Keith

last: Vance

institute: University of Bath

summary: These data show that Paupar, a CNS expressed long non-coding RNA (lncRNA), directly and functionally associates with KAP1, an essential epigenetic regulatory protein. Transcriptome profiling of N2A cells identified 1,913 differentially expressed genes whose expression significantly changed (at a 5% false discovery rate [FDR]) greater than 1.4-fold (log2 fold change ≈ 0.5) upon KAP1 depletion. Examination of the intersection of KAP1 and Paupar transcriptional targets showed that Paupar and KAP1 control expression of a shared set of target genes that are enriched for regulators of neuronal function and cell cycle in N2A cells. Furthermore, CHART-seq and ChIP-seq derived Paupar-KAP1 genome-wide co-occupancy maps revealed a 4-fold enrichment of overlap between Paupar and KAP1 bound sequences on chromatin.  This study also indicates that Paupar promotes KAP1 chromatin occupancy and H3K9me3 deposition at a subset of distal targets, through formation of a ribonucleoprotein complex containing Paupar, KAP1 and the PAX6 transcription factor. These observations provide important conceptual insights into the trans-acting modes of lncRNA-mediated epigenetic regulation and the mechanisms of KAP1 genomic recruitment.

overall_design: ChIP-seq analysis of KAP1 chromatin occupancy and microarray profiling of KAP1 target genes in N2A cells

first: Ioanna

last: Pavlaki

first: Farah

last: Alammari

first: Bin

last: Sun

first: Neil

last: Clark

first: Tamara

last: Sirey

first: Sheena

last: Lee

first: Dan

last: Woodcock

first: Chris

last: Ponting

first: Francis

last: Szele


title: A non-catalytic function of SETD1A regulates Cyclin K and the DNA damage response [RNA-seq]

first: Richard

last: Koche

summary: MLL/SET methyltransferases catalyze methylation of histone 3 lysine 4 and play critical roles in development and cancer. We assessed MLL/SET proteins and found that SETD1A is required for survival of acute myeloid leukemia (AML) cells. Mutagenesis studies and CRISPR-Cas9 domain screening, showed the enzymatic SET domain is not necessary for AML cell survival but that a newly identified region, termed the FLOS (Functional Location on SETD1A) domain, is indispensable. FLOS disruption suppresses DNA damage response genes and induces p53-dependent apoptosis. The FLOS domain acts as a Cyclin K-binding site that is required for chromosomal recruitment of Cyclin K, and for DNA repair-associated gene expression in S phase. These data identify a connection between the chromatin regulator SETD1A and the DNA damage response that is independent of histone methylation, and suggests that targeting SETD1A and Cyclin K complexes may represent a therapeutic opportunity for AML and potentially other cancers.

overall_design: RNA-seq of Setd1a knockout mouse MLL-AF9 leukemia cells and Ccnk shRNA-expressing mouse MLL-AF9 leukemia cells. Setd1aflox/flox;CreER and Setd1a+/+;CreER leukemia cells were analyzed at day 4 post-tamoxifen. shRNA-expressing mouse MLL-AF9 leukemia cells were analyzed at day 4 post-doxycycline.

first: Takayuki

last: Hoshii

first: Scott

last: Armstrong


title: Generation of matched patient-derived xenograft in vitro-in vivo models using 3D macroporous hydrogels for the study of liver cancer [WES]

status: Public on Jan 31 2018

city: St. John's

first: Touati

last: Benoukraf

state: NL

address: Craig L. Dobbin Genetics Research Centre,

department: Faculty of Medicine, Division of BioMedical Sciences

institute: Memorial University of Newfoundland

type: Genome variation profiling by high throughput sequencing

summary: Whole exome sequencing of matched patient-derived xenograft in vitro-in vivo models.

overall_design:
Comparison of genetic variants between matched patient-derived xenograft in vitro-in vivo models.

Submitter is depositing the processed data to an NCBI Variation database.

first: Eliza

last: Fong

first: Tan

middle: B

last: Toh

first: Xiaoxuan

last: Lin

first: Zheng

last: Liu

first: Lissa

last: Hooi

first: Masturah

last: Mohd Abdul Rashid

first: Edward

middle: K

last: Chow

first: The

middle: H

last: Huynh

first: Hanry

last: Yu