title: Total RNA-seq in ALL-SIL upon TLX1 knockdown

city: Ghent

first: Karen

last: Verboom

address: De Pintelaan 185

department: Pediatrics and Genetics

country: Belgium

institute: Ghent University

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive type of blood cancer resulting from malignant transformation of T-cell precursors. Several oncogenes, including the ‘T-cell leukemia homeobox 1’ TLX1 (HOX11) transcription factor, have been identified as early driver events that cooperate with other genetic aberrations in leukemic transformation of progenitor T-cells. The TLX1 controlled transcriptome in T-ALL has been investigated extensively in the past in terms of protein-coding genes, but remains unexplored thus far at the level of long non-coding RNAs (lncRNAs), the latter renown as well-established versatile and key players implicated in various cancer hallmarks. In this study, we present the first extensive analysis of the TLX1 regulated transcriptome focusing on lncRNA expression patterns. We present an integrative analysis of polyA and total RNA sequencing of ALL-SIL lymphoblasts with perturbed TLX1 expression and a primary T-ALL patient cohort (including 5 TLX1+ and 12 TLX3+ cases). We expanded our initially presented dataset of TLX1 and H3K27ac ChIP data in ALL-SIL cells (Durinck et al., Leukemia, 2015) with H3K4me1, H3K4me3, and ATAC-seq data to accurately define (super-) enhancer marked lncRNAs and assigned potential functional annotations to candidate TLX1-controlled lncRNAs through an in silico guilt-by-association approach. Our study paves the way for further functional analysis of selected lncRNAs as potential novel therapeutic targets for a precision medicine approach in the context of T-ALL.

overall_design: Total RNA-seq data was generated for the T-ALL cell line ALL-SIL upon TLX1 knockdown

first: Wouter

last: Van Loocke

first: Pieter-Jan

last: Volders

first: Bieke

last: Decaesteker

first: Jean

last: Soulier

first: Pieter

last: Van Vlierberghe

first: Jo

last: Vandesompele

first: Frank

last: Speleman

first: Kaat

last: Durinck


title: Integrin activation controls regulatory T cell-mediated peripheral tolerance

status: Public on Sep 13 2018

city: La Jolla

first: John

last: Chang

state: CA

address: 9500 Gilman Drive

department: School of Medicine

country: USA

institute: UCSD

type: Expression profiling by high throughput sequencing

summary: RNA sequencing analysis of Foxp3+YFP+ talin KO Treg cells compared to Foxp3+YFP+ wild-type Treg cells isolated from the spleen of 1-2 individual animals.

overall_design: Foxp3+YFP+ Treg cells were sorted by flow cytometry and libraries from 1-2 animals were prepared for RNA sequencing

first: Jane

middle: E

last: Klann

middle: T


title: Seh1 Interacts with Olig2 and Brd7 to Promote Oligodendrocyte Differentiation and Myelination

status: Public on Sep 12 2018

city: xiamen

first: Liu

last: Zhixiong

state: Fujian

address: Xiangan Nanlu 4221-120

department: School of Life Sciences

country: China

institute: Xiamen University

type: Genome binding/occupancy profiling by high throughput sequencing

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: PolyA+ RNA-seq in ALL-SIL upon TLX1 knockdown

status: Public on Sep 11 2018

overall_design: polyA+ RNA-seq data was generated for the T-ALL cell line ALL-SIL upon TLX1 knockdown


title: PolyA+ RNA-seq in a primary T-ALL patient cohort

overall_design: polyA+ RNA-seq data was generated for a primary T-ALL patient cohort


title: Total RNA-seq in ALL-SIL upon JQ1 inhibition

overall_design: Total RNA-seq data was generated for the T-ALL cell line ALL-SIL upon JQ1 inhibition


title: ATAC-seq of ALL-SIL cells

overall_design: ATAC-seq data was generated for the T-ALL cell line ALL-SIL


title: Transcriptomic profile of Fanconi anemia (FA) epidermal stem and progenitor cells (ESPCs)

city: Cincinnati

first: Sonya

middle: J

last: Ruiz-Torres

state: Ohio

address: 3333 Burnet Ave

department: Oncology

institute: Cincinnati Children's

summary: Squamous cell carcinoma (SCC) is a common cancer with global public health burden that arises from ESPCs in the skin or mucosa. To understand how genetic risk factors lay the foundation for SCC and develop effective prevention strategies, it is critical to understand the biology of ESPCs. Extreme predisposition to SCC is a hallmark of FA, an inherited disorder caused by germline loss-of-function mutations in any of 22 genes associated with the FA DNA repair pathway. Although DNA damage is the presumed cause, this does not explain the unique involvement of skin and mucosa as opposed to other solid tissues. To identify new epidermal vulnerabilities beyond DNA damage, we generated the first personalized model of FA epidermis. FA patient-derived induced pluripotent stem cells (PSCs) with a conditional FA pathway (+/-Doxycycline, DOX) were differentiated into ESPCs and 3D epidermis. The goal of this study is to uncover FA-dependent biological processes, performing transcriptome analyses of ESPCs in presence or absence of DOX in monolayer cultures.

overall_design: Examination of 2 FA patient-derived ESPC lines with conditional FA pathway (+/-DOX)

first: Marion

middle: G

last: Brusadelli

first: David

middle: P

last: Witte

first: Kathryn

middle: A

last: Wikenheiser-Brokamp

first: Sharon

last: Sauter

first: Adam

middle: S

last: Nelson

first: Mathieu

last: Sertorio

first: Timothy

middle: M

last: Chlon

last: Lane

first: Parinda

last: Mehta

first: Kasiani

middle: C

last: Myers

first: Dorothy

last: Supp

first: Paul

middle: F

last: Lambert

first: Kakajan

last: Komurov

first: Melinda

last: Butsch Kovacic

first: Stella

last: Davies

first: Susanne

middle: I

last: Wells


title: The IMiDs, through loss of Ikaros and Aiolos, primes myeloma cells for daratumumab mediated killing by upregulation of CD38

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University

summary: Recent studies have demonstrated that the immunomodulatory drugs (IMiDs) lead to the degradation of the transcription factors Ikaros and Aiolos. However, why their loss subsequently leads to multiple myeloma (MM) cell death remains unclear. Using CRISPR-Cas9 genome editing, we have deleted IKZF1 and IKZF3 in human MM cell lines to gain further insight into their downstream gene regulatory networks. Our findings strongly support the central role of Ikaros and Aiolos in the action of the IMiDs. Inactivation of either factor alone recapitulates the cell intrinsic action of the IMiDs, resulting in cell cycle arrest and induction of apoptosis. Furthermore, evaluation of the transcriptional changes resulting from their loss demonstrates striking overlap with lenalidomide treatment.

overall_design: RNA sequencing data of human multiple myeloma cell lines 72hrs post CRISPR-Cas9 deletion of IKZF1 or IKZF3, or treatment with Lenalidomide 10μM.

first: Pasquale

last: Fedele

first: Yang

last: Liao

first: Stephen

last: Nutt


title: H3K4me1 ChIP-seq in ALL-SIL

first: Karen

last: Verboom

overall_design: ChIP-seq data was generated for H3K4me1 in the T-ALL cell line ALL-SIL

first: Wouter

last: Van Loocke

first: Pieter-Jan

last: Volders

first: Bieke

last: Decaesteker

first: Jean

last: Soulier

first: Pieter

last: Van Vlierberghe

first: Jo

last: Vandesompele

first: Frank

last: Speleman

first: Kaat

last: Durinck


title: Hypercapnia Alters Expression of Immune Response, Nucleosome Assembly and Lipid Metabolism Genes in Differentiated Human Bronchial Epithelial Cells

city: Chicago

first: Marina

last: Casalino-Matsuda

address: 240 E Huron M340

institute: Northwestern University

summary: Hypercapnia, the elevation of CO2 in blood and tissues, commonly occurs in severe acute and chronic respiratory diseases, and is associated with increased risk of mortality. Recent studies have shown that hypercapnia adversely affects innate immunity, host defense, lung edema clearance, and cell proliferation. Airway epithelial dysfunction is a feature of advanced lung disease, but the effect of hypercapnia on airway epithelium is unknown. Thus, in the current study we examined the effect of normoxic hypercapnia (20% CO2 for 24 h) vs normocapnia (5% CO2), on global gene expression in differentiated normal human airway epithelial cells. Gene expression was assessed on Affymetrix microarrays, and subjected to gene ontology analysis for biological process and cluster-network representation. We found that hypercapnia downregulated the expression of 183 genes and upregulated 126. Among these, major gene clusters linked to immune responses and nucleosome assembly were largely downregulated, while lipid metabolism genes were largely upregulated.  The overwhelming majority of these genes were not previously known to be regulated by CO2. These changes in gene expression indicate the potential for hypercapnia to impact bronchial epithelial cell function in ways that may contribute to poor clinical outcomes in patients with severe acute or advanced chronic lung diseases.

overall_design:
Total 6 chips were used to analyze the effect of hypercapnia on NHBE cells. Triplicates for each condition (5% CO2 and 20% CO2 exposure for 24 hrs.)
CO2 Dose Response

first: S Marina

first: Naizhen

last: Wang

first: Peter

middle: H

last: Sporn


title: Single cell RNA Sequencing Analysis of Gene Expression Profile in Dgcr8 Conditional KO Embryonic Hearts

city: Beijing

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

institute: Tsinghua University

summary:
Purpose: To compare the single cell transcriptome of wild type and Mesp1Cre+/Dgcr8-/-  embryonic heart at embryonic stage E9.5
Methods: For single cell sample preparation, Ventricular part of E9.5 heart tubes were dissected and digested into single cells by 0.04% Trypsin combined with 0.05% Collagenase IV, and then transferred into DMEM containing 10% fetal bovine serum for termination. After washed in PBS without Ca2+, the single cells were manually transferred into cell lysis buffer with a mouth pipette. Total RNA was reverse transcribed and amplified using Smart-seq2 protocol (Picelli et al., 2014), followed by Tn5 tagmentation and PCR enrichment to generate libraries using TruePrep DNA Library Prep Kit V2 for illumina (Vazyme, TD501-503) according to the manufacturer’s suggested protocol. Clean reads were mapped to mouse genome (mm10) using Salmon.
Results: Genes significantly differentially expressed in the E9.5 Dgcr8 cKO single cardiomyocyte compared with wild type group were identified.
Conclusions: Dgcr8 cKO caused important gene expression changes in E9.5 cardiomyocytes at single cell level

overall_design: Perform single cell RNA-seq of wild type and Mesp1Cre+/Dgcr8-/- embryonic heart at embryonic stage E9.5

first: John

last: Doe


title: Activating PAX Gene Family Paralogs to Complement PAX5 Leukemia Driver Mutations

city: Seattle

first: Marshall

last: Horwitz

state: Washington

address: 850 Republican Street N431

department: Pathology

institute: University of Washington

summary: PAX5, one of nine members of the mammalian paired box (PAX) family of transcription factors, plays an important role in B cell development. Approximately one-third of individuals with pre-B acute lymphoblastic leukemia (ALL) acquire heterozygous inactivating mutations of PAX5 in malignant cells, and heterozygous germline loss-offunction PAX5 mutations cause autosomal dominant predisposition to ALL. At least in mice, Pax5 is required for pre-B cell maturation, and leukemic remission occurs when Pax5 expression is restored in a Pax5-deficient mouse model of ALL. Together, these observations indicate that PAX5 deficiency reversibly drives leukemogenesis. PAX5 and its two most closely related paralogs, PAX2 and PAX8, which are not mutated in ALL, exhibit overlapping expression and function redundantly during embryonic development. However, PAX5 alone is expressed in lymphocytes, while PAX2 and PAX8 are predominantly specific to kidney and thyroid, respectively. We show that forced expression of PAX2 or PAX8 complements PAX5 loss-of-function mutation in ALL cells as determined by modulation of PAX5 target genes, restoration of immunophenotypic and morphological differentiation, and, ultimately, reduction of replicative potential. Activation of PAX5 paralogs, PAX2 or PAX8, ordinarily silenced in lymphocytes, may therefore represent a novel approach for treating PAX5-deficient ALL. In pursuit of this strategy, we took advantage of the fact that, in kidney, PAX2 is upregulated by extracellular hyperosmolarity. We found that hyperosmolarity, at potentially clinically achievable levels, transcriptionally activates endogenous PAX2 in ALL cells via a mechanism dependent on NFAT5, a transcription factor coordinating response to hyperosmolarity. We also found that hyperosmolarity upregulates residual wild type PAX5 expression in ALL cells and modulates gene expression, including in PAX5-mutant primary ALL cells. These findings specifically demonstrate that osmosensing pathways may represent a new therapeutic target for ALL and more broadly point toward the possibility of using gene paralogs to rescue mutations driving cancer and other diseases.

overall_design: Reh cells were either transfected with a PAX paralog (PAX2, PAX5, PAX8, or empy vector pRRL-CMV-IRES-hrGFPII) or exposed to 80 mM salt (Potasium Gluconate or Calcium Chloride) for 24 hours. PolyA RNA from either two transfections or three salt exposures for each condition was combined to create mRNA profiles for each condition via deep sequencing.

first: Matthew

middle: R

last: Hart

first: Donovan

last: Anderson

first: Christopher

last: Porter

first: Tobias

last: Neff

first: Michael

last: Levin


title: Epigenetic and transcriptomic signature of aging in human liver [expression]

city: Bologna

first: Maria Giulia

last: Bacalini

address: Via Altura 3

department: Brain Aging Laboratory

country: Italy

institute: IRCCS Istituto delle Scienze Neurologiche di Bologna

summary: Gene expression profiling of liver biopsies collected from 33 healthy liver donors ranging from 13 to 90 years old. The Affymetrix HG-U133 Plus 2.0 GeneChip platform was used to evaluate gene-expression.

overall_design: Total RNA (including miRNAs) was extracted using the mirVana miRNA Isolation Kit (Ambion); cDNA synthesis, biotin-labelled target synthesis, hybridization, staining and scanning were performed according to Affymetrix standard protocol.

first: Maria

first: Claudio

last: Franceschi

first: Davide

last: Gentilini

first: Francesco

last: Ravaioli

first: Xiaoyuan

last: Zhou

first: Daniel

last: Remondini

first: Chiara

last: Pirazzini

first: Cristina

last: Giuliani

first: Elena

last: Marasxo

first: Noémie

last: Gensous

first: Anna

last: Di Blasio

first: Ewa

last: Ellis

first: Roberto

last: Gramignoli

first: Gastone

last: Castellani

first: Miriam

last: Capri

first: Stephen

last: Strom

first: Christine

last: Nardini

first: Matteo

last: Cescon

first: Gian

middle: L

last: Grazi

first: Paolo

last: Garagnani


title: Epigenetic and transcriptomic signature of aging in human liver [methylation]

first: Maria Giulia

last: Bacalini

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of liver biopsies collected from 45 healthy liver donors ranging from 13 to 90 years old. The Infinium HumanMethylation450 BeadChip was used to obtain DNA methylation profiles across approximately 470,000 CpGs.

overall_design: DNA was bisulfite-converted using the EZDNA Methylation-Gold Kit (Zymo Research) and analysed using the Infinium HumanMethylation450 BeadChip (Illumina) following manufacturer's instructions.

first: Maria

first: Claudio

last: Franceschi

first: Davide

last: Gentilini

first: Francesco

last: Ravaioli


title: Epigenetic and transcriptomic signature of aging in human liver


title: Molecular Determinants of Post-Mastectomy Breast Cancer Recurrence

status: Public on Sep 14 2018

city: Houston

first: Funda

last: Meric-Bernstam

state: TX

address: 1400 Pressler St.

department: Invest. Cancer Therapeutics

institute: The University of Texas MD Anderson Cancer Center

summary: Breast cancer (BC) adjuvant therapy after mastectomy in the setting of 1-3 positive lymph nodes has been controversial. This retrospective Translational Breast Cancer Research Consortium study evaluated molecular aberrations in primary cancers associated with locoregional recurrence (LRR) or distant metastasis (DM) compared to non-recurrent controls.  We identified 115 HER2 negative, therapy naïve, T 1-3 and N 0-1 BC patients treated with mastectomy but no post-mastectomy radiotherapy.  This included 32 LRR, 34 DM and 49 controls. RNAseq was performed on primary tumors in 110 patients; with no difference in RNA profiles between patients with LRR, DM or controls.  DNA analysis on 57 primary tumors (17 LRR, 15 DM and 25 controls) identified significantly more NF1 mutations and mitogen activated protein kinase (MAPK) pathway gene mutations in patients with LRR (24%, 47%) and DM (27%, 40%) compared to controls (0%, 0%; p<0.0001 and p=0.0070, respectively).  Three patients had matched primary vs LRR samples, one patient had a gain of a NF1 mutation in the LRR.  There was no significant difference between the groups for PTEN loss or cleaved caspase 3 expression.  The mean percentage Ki 67 labeling index was higher in patients with LRR (29.2%) and DM (26%) versus controls (14%,p= 0.0045).  In summary, mutations in the MAPK pathway, specifically NF1, were associated with both LRR and DM, suggesting that alterations in MAPK signaling are associated with a more aggressive tumor phenotype.  Validation of these associations in tissues from randomized trials may support targeted therapy to reduce breast cancer recurrence.

overall_design: This is a multicenter retrospective study of patients who underwent mastectomy at a participating Translational Breast Cancer Research Consortium (TBCRC) institution.  Study centers included Memorial Sloan Kettering Cancer Center, University of Pittsburgh, Duke University, Dana Farber Cancer Institute, University of North Carolina at Chapel Hill, Georgetown University, University of Michigan at Ann Arbor, Vanderbilt University, University of Alabama at Birmingham and MD Anderson Cancer Center.  Eligible patients included those patients who underwent mastectomy without radiation for T stage 1-3 and N stage 0-1 breast cancer, and for whom archived tissues and outcome data were available. Patients with any recurrence, loco-regional (LRR) or with distant metastasis (DM), were treated from 1997 to present time as this was felt to represent an era when treatment recommendations would be the most uniform and consistent. Patients with LRR could have a subsequent DM as long as this DM was diagnosed at least 3 months after the LRR. Patients who developed LRR after developing distant metastases were placed in the DM group. Control patients were treated from 1997 to 2007 to allow at least five years follow-up with a disease-free interval.  Controls were matched to cases for age, ER/PR status, chemotherapy and endocrine therapy regimens and year of diagnosis.  All patients were treated with an upfront mastectomy followed by systemic therapy if indicated, which included chemotherapy, endocrine therapy or both.  Patients were ineligible if they received post-mastectomy radiation therapy, neoadjuvant chemotherapy, had a T4 primary tumor, N2 nodal disease, were HER2 positive, had positive margins after mastectomy, had fewer than 10 lymph nodes retrieved at axillary lymph node dissection, or had inadequate follow-up (<5 years) if a control patient.  If specimens were available from the recurrent tumors, these were also collected for exploratory analysis.

first: Kimberly

last: Keene

first: Tari

last: King

first: E

last: Hwang

first: Bo

last: Peng

first: Kandace

last: McGuire

first: Coya

last: Tapia

first: Hong

last: Zhang

first: Sejong

last: Bae

first: Faina

last: Nakhlis

first: Nancy

last: Klauber-Demore

first: Ingrid

last: Meszoely

first: Michael

last: Sabel

first: Shawna

last: Willey

first: Agda

middle: K

last: Eterovic

first: Cliff

last: Hudis

first: Antonio

last: Wolff

first: Jennifer

last: De Los Santos

first: Alastair

last: Thompson

first: Gordon

middle: B

last: Mills

last: Bernstam


title: Nuclear transcriptomes of the seven neuronal cell types that constitute the Drosophila mushroom bodies

status: Public on Sep 10 2018

city: Bethesda

first: Fred

middle: P.

last: Davis

state: MD

address: 9000 Rockville Pike

department: NIAMS

institute: NIH

summary: The insect mushroom body (MB) is a conserved central brain structure that receives multi-modal inputs and plays key roles in a diverse array of behaviors.  In Drosophila melanogaster, the MB has served as the primary invertebrate model to investigate how neural circuits underlie plasticity related to memory formation and storage.  A vast literature describes the development, morphology, wiring, and function of each of the MB cell types as well as their inputs and outputs.  MBs consist of approximately 2000 intrinsic Kenyon Cells per hemisphere that are divided into three major neuron classes — γ, α′/β′ and α/β — based on their birth order, morphology and connectivity.  These classes are further sub-divided into 7 cell subtypes — γd, γm, α′/β′ap, α′/β′m, α/βp, α/βs and α/βc. A wealth of functional studies demonstrate that these 7 MB cell subtypes connect to different input and output neurons and play distinct roles in memory processing.   The functional differences between these cell subtypes are presumably reflected in unique transcriptional programs, although this has not been investigated.  Here, we used RNA sequencing (RNA-seq) to profile the nuclear transcriptomes of each of the 7 MB neuronal cell subtypes. We identified 350 MB class- or subtype-specific genes.  These include the widely used α/β class marker Fas2 and the α′/β′ class marker trio. Immunostaining data corroborates the RNA-seq measurements at the protein level for several cases. Importantly, our data provide a full accounting of the neurotransmitter receptors, transporters, neurotransmitter biosynthetic enzymes, neuropeptides, and neuropeptide receptors expressed within each of these cell types. This high-quality, cell type-level transcriptomic catalog for the Drosophila MB provides a valuable resource for the fly neuroscience community.

overall_design: 14 nuclear RNA-seq samples prepared from biological duplicates of seven Kenyon cell subtypes using the TAPIN protocol.

first: Meng-Fu

last: Shih

first: Gilbert

last: Henry

first: Josh

last: Dubnau


title: Coronary artery disease genes SMAD3 and TCF21 promote opposing interactive genetic programs that regulate smooth muscle cell differentiation and disease risk [ChIP-seq]

city: Stanford

first: Thomas

last: Quertermous

address: 300 Pasteur Drive

department: Medicine Cardiology

institute: Stanford University

summary: Although numerous genetic loci have been associated with coronary artery disease (CAD) with genome wide association studies (GWAS), efforts are needed to identify the causal genes in these loci and link them into fundamental signaling pathways. Toward that end, experiments reported here extend our investigation of the disease mechanism of CAD associated gene SMAD3, a central transcriptional intermediate in the TGFb pathway, investigating its role in smooth muscle biology. In vitro studies in human coronary artery smooth muscle cells (HCASMC) revealed that SMAD3 modulates cell state decisions in this cell type, promoting expression of differentiation marker genes and migration while inhibiting proliferation. RNA and chromatin immunoprecipitation sequencing (ChIPseq) studies in HCASMC identified downstream genes that reside in pathways which mediate vascular development and disease processes, including those related to atherosclerosis pathophysiology, expanding understanding of the TGFb canonical pathway in this cell type. ChIPseq studies also found colocalization of SMAD3 binding in loci targeted by TCF21, a CAD associated transcription factor that has been shown to produce a CAD protective de-differentiation program in HCASMC. In loci where these factors are juxtaposed on DNA, SMAD3 binding was anti-correlated with TCF21, and increased in cells depleted of TCF21, as shown by ChIPseq and ChIP experiments. Further, reporter gene studies revealed that while SMAD3 increased transcription at a SERPINE1 enhancer, and this effect was blocked by TCF21. Together, these data suggest that SMAD3 regulation of gene expression is modulated by TCF21, through independent regulation of jointly occupied genes and through epigenetic and possibly direct protein-protein interactions. Finally, eQTL studies in HCASMC indicated that SMAD3 expression is directly associated with increased disease risk, opposing the known protective effect of TCF21. We propose that the pro-differentiation function of SMAD3 inhibits HCASMC dedifferentiation of these cells as they respond to vascular stresses and expand and migrate to stabilize the plaque, and that SMAD3 function is directly opposed at the transcriptional level by the disease protective expression of TCF21, which promotes dedifferentiation and phenotypic modulation.

overall_design:
Human coronary artery smooth muscle cells (HCASMC) grown in serum were evaluated with an antibody to SMAD3, or IgG control.

This series includes the re-analysis of GSM1246721. The processed data for this anti-SMAD3 ChIP sample in A549 cells are available at the foot of this record.

first: Dharini

last: Iyer

first: Quanyi

last: Zhao


title: Dynamic turnover of paused pol II complexes at human promoters

city: Aurora

first: David

last: Bentley

state: Colorado

department: BMG

institute: UCD AMC

summary: Paused RNA polymerase II that piles up near most human promoters is the target of mechanisms that control entry into productive elongation.  Whether paused pol II is a stable or a dynamic target remains unresolved. We report that most 5’-paused pol II throughout the genome is turned over within 2 minutes. This process is revealed under hypertonic conditions that prevent pol II recruitment to promoters. This turnover requires cell viability but is not prevented by inhibiting transcription elongation suggesting that it is mediated at the level of termination. When initiation was prevented by triptolide during recovery from high salt, a novel pre-initiated state of pol II lacking the pausing factor Spt5 accumulated at transcription start sites. We propose that pol II occupancy near 5’ ends is governed by a cycle of ongoing assembly of pre-initiated complexes that transition to pause sites followed by eviction from the DNA template. This model suggests that mechanisms regulating the transition to productive elongation at pause sites operate on a dynamic population of pol II that is turning over at rates far higher than previously suspected. We suggest that a plausible alternative to elongation control via escape from a stable pause, is by escape from premature termination.

overall_design: Initiation of transcription was inhibited by high salt treatment or treatment with triptolide and pol II occupancy was mapped around start sites and within genes by anti-pol II ChIP-seq in HCT116 cells at time points between 2 and 10 minutes afterwards.

first: Ben

last: Erickson


title: BCAT1 and miR-2504: novel methylome signature distinguishes spindle/desmoplastic melanoma from superficial malignant peripheral nerve sheath tumor

city: New York

first: Varshini

last: Vasudevaraja

state: NY

address: 550 1st Avenue

institute: NYU Langone Health

summary:
Genome wide methylation of superficial malignant peripheral nerve sheath tumors and spindle cell melanomas. EPIC HD 850K array is used to identifiy differentally methylated promoter region probes and unique methyome signatures.
Superficial/cutaneous malignant peripheral nerve sheath tumor (c-MPNST) is a rare, soft tissue neoplasm that shares morphological, immunohistochemical and molecular with spindle and desmoplastic melanoma (SDM). Herein we investigate a methylome signature distinguishing between both entities.  DNA from formalin-fixed, paraffin-embedded (FFPE) tissues was extracted and processed using the Illumina Infinium epic array interrogating 866,562 CpG sites. Using a home grown informatics pipeline we identify differentially methylated regions (DMR) between both entities. Functional network analysis for enrichment signatures was performed using DAVID tools. Identified DMR’s are compared with TCGA skin cutaneous melanoma (SKCM) data and a recently published set of MPNST in order to assess specifity of the identified signature.   Thirty patients are included (SDM= 15 and c-MPNST=15) including 23 males and 7 females. Unsupervised hierarchical clustering probes showed a distinct pattern of methylation between c-MPNST and SDM. Two probes cg20783223 and cg13332552 co-localized in the promoter region of BCAT1 and MIR2504. Pathway analysis highlighted an enrichment in s subset of genes involved in breast and gastric cancer centered on BCAT1 and downstream activated genes in the mTORC pathway.    Our study identifies BCAT1 as a unique marker distinguishing between SDM and MPNST. Further immunohistochemical studies are underway to investigate the role of BCAT expression in that regard.

overall_design: Two sets of tumors including 15 MPNST and 15 SDM's are analyzed.

first: George

last: Jour


title: Transcriptome analysis of U87 cells upon LINC00152 knockdown

city: Charlottesville

first: Anindya

last: Dutta

state: VA

address: 1300 Jefferson Park Ave

department: Biochemistry & Molecular Genetics

institute: University Of Virginia

summary: To understand the global changes in genes expression after knockdown of LINC00152, we compared transcriptomes of control cells (treated with siGL2) and LINC00152 knockdown cells (treated with si00152).

overall_design: U87 cells were transfected during two rounds of transfection. First, cells were reverse transfected with a combination of two LINC00152 siRNAs or a nonspecific siGL2 control siRNA using Lipofectamine RNAiMAX transfection reagent. 24 hours later, a second round of transfection was performed using the same reagents. 24 hours after the final transfection, cells were harvested and used for library preparation.

first: Brian

last: Reon

first: Bruno

last: Karia

first: Manjari

last: Kiran


title: RIP1 Kinase Drives Macrophage-Mediated Adaptive Immune Tolerance in Pancreatic Cancer

summary: Gene ontology analysis suggested that targeting RIP1 induced changes in diverse innate inflammatory processes. Ingenuity analysis demonstrated that pathwaysupregulated by RIP1i included both MAP kinase and PPAR signaling, whereas select apoptosis and phagocytosis pathways were inhibited.

overall_design: Compare the landscape of transcriptome of bone marrow derived macrophage following treatment of RIP1i vs. control

first: Wei

last: Wang

last: Miller


title: Transcriptional profiles of normal human mature B cells

first: Riccardo

last: Dalla-Favera

address: 1130 St Nicholas Avenue

institute: Columbia University

summary: Mature B cells leave the bone marrow  as naïve B cells and migrate to the secondary lymphoid organs where they encounter the antigen for the first time. This interaction stimulates B cells to rapidly grow and form characteristic histological structures called germinal center. In the germinal centers, B cells are targeted by mechanisms of genetic editing of the immunoglobulin loci, namely somatic hypermutation and class switch recombination, undergo selection for high affinity immunoglobulin receptors and are committed to differentiate into memory B cells or plasma cells. GCs display two histological areas the dark and the light zone that have been characterized as functionally distinct compartments through which B cells recycle multiple times during the germinal center reaction.

overall_design: Naïve, germinal center and memory B cells were isolated from three independent donors each.

first: Katia

last: Basso

first: Antony

last: Baden Holmes


title: RNA expression in postnatal mouse ventricular tissue

city: Helsinki

first: Virpi

last: Talman

address: P.O. Box 56 (Viikinkaari 5E)

department: Faculty of Pharmacy

country: Finland

institute: University of Helsinki

summary: Mammals lose the ability to regenerate their hearts within one week after birth. During this regenerative window, cardiac energy metabolism shifts from glycolysis to fatty acid oxidation, and recent evidence suggests that metabolism may participate in controlling cardiomyocyte cell cycle. However, the molecular mechanisms mediating the loss of postnatal cardiac regeneration are not fully understood. This study aims at providing an integrated resource of mRNA, protein and metabolite changes in the neonatal heart to identify metabolism-related mechanisms associated with the postnatal loss of regenerative capacity. Mouse ventricular tissue samples taken on postnatal days 1, 4, 9 and 23 (P01, P04, P09 and P23, respectively) were analyzed with RNA sequencing (RNAseq) and global proteomics and metabolomics. Differential expression was observed for 8547 mRNAs and for 1199 of the 2285 quantified proteins. Furthermore, 151 metabolites with significant changes were identified. Gene ontology analysis, KEGG pathway analysis and fuzzy c-means clustering were used to identify biological processes and metabolic pathways either up- or downregulated on all three levels. This is the first systems-level resource combining data from genome-wide transcriptomics with global quantitative proteomics and untargeted metabolomics analyses of the mouse heart throughout the early postnatal period. This integrated multi-level data of molecular changes associated with the loss of cardiac regeneration may open up new possibilities for the development of regenerative therapies.

overall_design: RNA sequencing was carried out with three pooled samples (each from 3 hearts) at each time point - i.e. 1, 4, 9 and 23 days after birth.

first: Jaakko

last: Teppo

first: Päivi

last: Pöhö

first: Parisa

last: Movahedi

first: Anu

last: Vaikkinen

first: Tuuli

last: Karhu

first: Kajetan

last: Trost

first: Tommi

last: Suvitaival

first: Jukka

last: Heikkonen

first: Tapio

last: Pahikkala

last: Kotiaho

first: Risto

last: Kostiainen

first: Markku

last: Varjosalo

first: Heikki

last: Ruskoaho


title: MEF2B chromatin binding in normal and malignant B cells

last: Dalla-Favera

summary: The MEF2B transcription factor is recurrently mutated in germinal-center (GC)-derived B-cell lymphomas, but its role in normal and neoplastic GC development is unknown. Here we identify MEF2B transcriptional targets in GC, which indicate its control of cell proliferation, apoptosis, GC confinement and differentiation. Consistently, Mef2b deletion reduces GC formation in mice. The most common tumor-associated MEF2B mutant (MEF2BD83V) is hypomorphic, but escapes binding and negative regulation by Cabin1 and HDACs. Mef2bD83V expression leads to GC enlargement and GC-derived tumors in 25% of the animals. This phenotype becomes fully penetrant in combination with BCL2 de-regulation, an event commonly associated with MEF2B mutations in human lymphoma. These results identify MEF2B as a critical GC regulator, and as a dominant oncogene in lymphomagenesis.

overall_design: ChIP-seq analyses of MEF2B bound regions in normal human germinal center B cells and in lymphoma cell lines.

last: Holmes


title: Cellular and Molecular Targeting of Recurrence in Acute Myeloid Leukemia

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

department: Stem Cell and Cancer Research Institute (SCC-RI)

country: Canada

institute: McMaster University

summary: While disease recurrence remains the outstanding clinical challenge in acute myeloid leukemia (AML), the basis of relapse remains poorly characterized and thereby preventing effective therapeutic targeting. We performed gene expression analysis of human AML patient samples in addition to in vitro and in vivo assays of leukemic cell survival and self-renewal using xenograft modeling. These molecular and functional analyses afforded the identification of unique target genes that support recurrence. Preclinical modeling using these novel targets provided proof-of-principle for combination therapies towards more effective and durable suppression of AML regrowth.

overall_design: AML samples were obtained from patients belonging to intermediate- and high-risk prognostic groups and healthy hematopoietic cells were obtained from mobilized peripheral blood (MPB) or bone marrow (BM) of healthy donors. Xenotransplant assays were performed by intravenous injection of primary human samples into sub-lethaly irradiated immunodefcient mice. RNA was purified from healthy MNCs, FACS-purified patient leukemic blasts (based on side scatter and CD45 intensity) and from xenografts purified from the recipient mouse BM. Transcriptional profiles were compared after AraC-based chemotherapy at post-induction or relapse, relative to untreated diagnostic samples in human patients. AraC cytoredutive therapy was simulated In xenografts assays and gene expression was analyzed post induction or at relapse compared to saline-treated matched xenografts as control.

first: Allison

last: Boyd

first: Lili

last: Aslostovar

first: Aline

last: Fiebig-Comyn

first: Zoya

last: Shapovalova

first: Mohammed

last: Almakadi

first: Jenniffer

last: Reid

first: Fanny

last: Casado

first: Kyle

last: Salci

first: Anargyros

last: Xenocostas

first: Ronan

last: Foley

first: Brian

last: Leber


title: Beta-catenin dependent gene expression

status: Public on Sep 09 2018

first: Tzu Lip

last: Phang

state: CO

address: 12700 East 19th Avenue

department: Medicine

institute: University of Colorado, Denver

summary:
Gene experssion was evaluated in the lungs of mice in which beta-catenin was stabilized or knocked out in the SCGB1A1 lineage.
Gene expression was assayed on post-natal day 21

overall_design: Each group contained 4 mice

first: Susan

middle: D

last: Reynolds


title: Germinal Center B cell transcriptional profiles in Mef2b mouse models

first: Riccardo

overall_design: The dataset includes: wild-type mice (WT); mice expressing only 1 Mef2b allele in GC B cells (HET); mice lacking Mef2b expression (KO); mice expressing 1 wt and 1 mutant Mef2b allele in GC B cells (D83V); mice expressing only 1 mutant Mef2b allele in GC B cells (KO-D83V). Three to four mice for each genotype have been analyzed.

first: Katia

last: Basso

first: Antony

last: Baden Holmes


title: Profiling of escape kinetics of viruses subjected to RNAi

first: Benjamin

last: tenOever

address: 1468 Madison Avenue

department: Microbiology

institute: Ichan School of Medicine at Mount Sinai

summary: To assess how viruses of different genome compositions escape engineered RNAi

sample_organism:
Homo sapiens
Canis lupus familiaris
Mesocricetus auratus

overall_design:
mRNA profiles and alignments to viral genomes of BHK-21, RNaseIII-/-, and MDCK cells infected with Sindbis viruses, Semliki Forest viruses, Sendai viruses, or Influenza A viruses that were either a control or subjected to RNAi

mRNA profiles and alignments to viral genomes of 293T and RNaseIII-/- cells infected with Polioviruses viruses that were either a contol or subjected to RNAi


title: Genetic modifier of TGF-beta1 stimulated pulmonayr fibrosis

city: Providence

first: Chun Geun

last: Lee

state: RI

address: 185 Meeting St

department: Molecular Microbiology and Immunology

institute: Brown University

summary: Expression profiling of pulmonayr fibrosis prone  and fibrosis resistant strains of mice with transgenic overexpression of TGF-beta1

overall_design: Expression analysis using lung total RNAs  prepared from 3 fibrosis prone (AKR/J, A/J, C57BL6/J) and 3 fibrosis-resisitant (Balb/cJ, 3C3H/J, 129Si/J) TGF-beta1 trasgenic (Tg) mice

first: Jack

last: Elias

first: Chun

first: Chang-Min


title: RNA-seq of HBV-infected Primary Human Hepatocytes treatment by Tazarotene

city: Shanghai

first: Baocun

last: Li

address: Medical College Road 138

institute: Fudan University

summary: Monitor HBV mRNA reduction in response to Tazarotene and to identify global transcriptome-wide gene expression associated with Tazarotene treatment in HBV infected PHH using RNA-Seq

overall_design: HBV infected PHH treated with Tazarotene 1 μM or DMSO, time points 8h, 48h

first: Yang

last: Wang

first: Zhenghong

last: Yuan

first: Jieliang

last: Chen


title: Defective transcription elongation in a subset of cancers confers immunotherapy resistance (BGI12 RNA-Seq)

status: Public on Sep 08 2018

first: Kakajan

last: Komurov

state: OH

address: 3333 Burnet Ave OH 45229

department: Division of Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital

summary: The nature and the role of global transcriptional deregulations in cancers are not fully understood. We report a phenotype in a significant portion of cancers characterized by widespread defects in mRNA transcription elongation (TE). Cancers with TE defects (TEdeff) were characterized by spurious transcription and defective mRNA processing, specifically in a large set of genes characterized by long genomic length, poised promoters and inducible expression. As such, signaling pathways regulated by such genes, such as interferon/JAK/STAT and TNF/NF-κB pathways, were consistently suppressed in TEdeff tumors. Remarkably, TEdeff significantly correlated with the poor response and outcome in immunotherapy, but not chemo- or targeted therapy, -treated renal cell carcinoma and metastatic melanoma patients in 4 different cohorts. Importantly, forced pharmacologic or genetic induction of TEdeff in tumor cells impaired the expression of the interferon/JAK/STAT and TNF/NF-κB pathways, and imposed resistance to the innate and adaptive anti-tumor immune responses and checkpoint inhibitor therapy in vivo. Therefore, defective TE is a novel epigenetic mechanism in the tumor arsenal of immune resistance tools, which warrants its assessment in cancer patients undergoing immunotherapy.

first: Vishnu

last: Modur

first: Navneet

last: Singh

first: Vakul

last: Mohanty

first: Eunah

last: Chung

first: Belal

last: Muhammad

first: Kwangmin

last: Choi

first: Xiaoting

first: Kashish

last: Chetal

first: Nancy

last: Ratner

first: Nathan

last: Salomonis

first: Matthew

middle: T

last: Weirauch

last: Waltz

first: Gang

last: Huang

first: Lisa

last: Privette-Vinnedge

first: Joo-Seop

last: Park

first: Edith

last: Janssen


title: Defective transcription elongation in a subset of cancers confers immunotherapy resistance (human ChIP-Seq)

overall_design: Chip sequencing was performed on UACC-812 (transcription elongation defects Tedeff +ve) cancer cell line and T47D (transcription elongation defects Tedeff -ve) cell ine to quantiufy the effect that transcriptional elongation defect has on genome wide distribution of RNA pol2 and RNA pol2-Ser5 in cancers.

last: Chen

first: Susan


title: Defective transcription elongation in a subset of cancers confers immunotherapy resistance

first: Kakajan

last: Komurov

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: S. flexneri transcriptome in Henle-407 cells

city: Kalamazoo

first: Ben

middle: James

last: Koestler

state: MI

address: 1903 West Michigan Avenue, 3119 Wood Hall

department: Biological Sciences

institute: Western Michigan University

summary: S. flexneri infected Henle-407 cells were treated with and without 20 mM formate, RNA-seq was used to determine transcriptome changes

sample_organism:
Homo sapiens
Shigella flexneri 2a str. 2457T

overall_design: S. flexneri 2457T WT, Henle-407 cells as host, ± 20 mM formate, mock control

first: Benjamin

middle: J

first: Shelley

last: Payne


title: Extraction-Free Whole Transcriptome Profiling from Specific Subareas of Unstained or H&E Stained FFPE Tissues

city: Carlsbad

first: Milos

last: Babic

address: 5922 Farnsworth Court, Suite 102

institute: BioSpyder Technologies Inc.

summary: We describe the use of a ligation-based targeted whole transcriptome expression profiling assay, TempO-Seq™, to profile formalin-fixed paraffin-embedded (FFPE) tissue, including H&E stained FFPE tissue, by directly lysing tissue scraped from slides without extracting RNA or converting the RNA to cDNA. The correlation of measured gene expression changes in unfixed and fixed samples using blocks prepared from a pellet of a single cell type was R2 = 0.97, demonstrating that no significant artifacts were introduced by fixation. Fixed and fresh samples prepared in an equivalent manner produced comparable sequencing depth results (+/- 20%), with similar %CV (11.5 and 12.7%, respectively), indicating no significant loss of measurable RNA due to fixation. The sensitivity of the TempO-Seq assay was the same whether the tissue section was fixed or not. The assay performance was equivalent for human, mouse, or rat whole transcriptome. The results from 10 mm2 and 2 mm2 areas of tissue obtained from 5 μm thick sections were equivalent, thus demonstrating high sensitivity and ability to profile focal areas of histology within a section. Replicate reproducibility of separate areas of tissue ranged from R2= 0.83 (lung) to 0.96 (liver) depending on the tissue type, with an average correlation of R2 = 0.90 across nine tissue types. The average %CV’s were 16.8% for genes expressed at greater than 200 counts, and 20.3% for genes greater than 50 counts. Tissue specific differences in gene expression were identified and agreed with the literature. There was negligible impact on assay performance using FFPE tissues that had been archived for up to 30 years. Similarly, there was negligible impact of H&E staining, facilitating accurate visualization for scraping and assay of small focal areas of specific histology within a section.

sample_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: FFPE tissues and cell pellets from human, mouse, and rat were used to assess performance of a targeted whole transcriptome expression profiling method. A subset of human FFPE tissue was stained with hemotoxylin and eosin. Another subset of human FFPE tissue was pulled from archives and were greater than 24 years old at the time of processing. A subset of rat tissue was fixed for variable amounts of time before embedding. Various amounts of FFPE tissue was used as input into the assay. For all FFPE samples, FFPE tissue was used as direct input into the assay without RNA extraction. Twelve samples are FFPE formed by fixing, embedding, and sectioning pellets from cultured MCF7 and MDA-MB-231 cells. Six samples (marked "fresh") are lysates of unfixed cells processed through the same assay for comparison.

first: Christy

last: Trejo

first: Miloš

last: Babić


title: Transcriptome profile of murine endometrial cancer cell lines

city: Cleveland

first: Daniel

last: McGrail

address: 9500 Euclid Avenue

department: Center for Immunotherapy and Precision Immuno-Oncology

institute: Cleveland Clinic

summary: Mouse endometrial cancer cell lines with PTEN deletion/mutant KRAS expression (MEC.PK) or MSH2 deletion (21B)

overall_design: Two cell lines run in duplicate

first: D

first: S

last: Lin


title: RNA-seq analysis comparing gene expression in Drosophila sea mutants and controls

status: Public on Sep 07 2018

city: Bloomington

first: Jason

last: Tennessen

state: IN

address: 1001 E. Third St

department: Department of Biology

institute: Indiana University

summary: The goal of this study was to determine how decreased mitochondrial citrate export influences gene expression in Drosophila larvae. RNA was isolated from Drosopohila sea mutants, which exhibiti decreased mitochondrial citrate transport activity, and a genetically-matched control strain during mid-L3 development.

overall_design: Larvae were collected as described in Li, H., Tennessen, J. M. Preparation of Drosophila Larval Samples for Gas Chromatography-Mass Spectrometry (GC-MS)-based Metabolomics. J. Vis. Exp. (136), e57847, doi:10.3791/57847 (2018). RNA was purified from staged mid-L3 larvae using a RNeasy Mini Kit (Qiagen). Sequencing was performed using an Illumina NextSeq500 platform with 75 bp sequencing module generating 41 bp paired-end reads. After the sequencing run, demultiplexing was performed with bcl2fastq v2.20.0.422.

first: Hongde

last: Li


first: Michaela

last: Willi

department: NIDDK

institute: NIH

summary: V5 tagged Elf5.

overall_design: ChIP-seq for V5 in the mammary tissues of Elf5-V5 mice.

first: Hye

last: Lee


title: Quantitative analysis of transcriptome and H3K9me3 binding profiles in wild type and tumorous ovaries

city: Boston

first: Mitzi

last: Kuroda

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Brigham and Women's Hospital/Harvard Medical School


title: Next Generation Sequencing to Facilitate Quantitative Analysis of wild type, setdb1 GLKD and snf[148] ovary H3K9me3 binding profiles [ChIP-seq]

summary: Comparison of wild type, setdb1 GLKD, and snf[148] H3K9me3 profiles shows that SXL facilitates H3K9me3 deposition on SETDB1 regulated genes

overall_design: H3K9me3 ChIP reads from ovaries in 0-24 hour virgin wild type and 3-5 day old ovaries from setdb1 GLKD and snf[148] mutants were generated by next generation sequencing, in duplicate, using Illumina HiSeq2500

first: Helen

last: Salz


title: Expression data from hela cells stable clones overexpressing TFEB-GFP

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

summary:
In order to identify the effects of TFEB overexpression on the hela cells transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the hela TFEB stable clones
Transcriptome analysis of hela stable clones overexpressing TFEB-GFP

overall_design: For the analysis on the hela stable clones overexpressing TFEB, total RNA was extracted from the cells of three biological replicates; RNA extracted from hela WT cells was used as control.


title: Next Generation Sequencing to Facilitate Quantitative Analysis of wild type, setdb1 GLKD, wde GLKD, and hp1a GLKD transcriptomes [RNA-seq]

summary: Comparison of wild type, setdb1 GLKD, wde GLKD, and hp1a GLKD reveals loss of H3K9me3 chromatin modifiers derepresses spermatogenesis genes

overall_design: Total mRNA reads from ovaries from wild tyep, setdb1 GLKD, wde GLKD, and hp1a GLKD were generated by next generation sequencing, in duplicate, using Illumina HiSeq2500


title: Defective transcription elongation in a subset of cancers confers immunotherapy resistance (B16 RNA-Seq)

city: Cincinnati

first: Kakajan

overall_design: RNAseq was used to profile expression patterns in human (cancer cell lines and tumor tissues) and flavopiridol,a CDK9 inhibitor, treated mouse B16-F10 cell lines to identify and characterize Tedeff cancers. We also performed RNApol2 and RNApol2-ser5 chipseq to study the genome wide distribution of RNA polymerase 2 in TEdeff canmcer cell lines vs control cancer cell lines

first: Vishnu

last: Modur

first: Navneet

last: Singh

first: Vakul

last: Mohanty

first: Eunah

last: Chung

first: Belal

last: Muhammad

first: Kwangmin

last: Choi

first: Xiaoting

first: Kashish

last: Chetal

first: Nancy

last: Ratner

first: Nathan

last: Salomonis

first: Matthew

last: Weirauch

first: Susan

last: Waltz

first: Gang

last: Huang

first: Lisa

last: Privette-Vinnedge

first: Joo-Seop

last: Park

first: Edith

last: Janssen


status: Public on Sep 06 2018

first: Feng

last: Liu

address: 600 Yishan Road

department: Department of Otolaryngology-Head and Neck Surgery

institute: Shanghai JiaoTong University Affiliated Sixth People's Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: The peritoneal macrophages were infected with Mtb H37Rv for 4 hours, and the miRNA expression profile were analyzed with deep sequencing.

overall_design: miRNA profiles of Mtb H37Rv infected peritoneal macrophages and uninfected controls were generated by deep sequencing, in triplicate.

first: Baoxue

last: Ge


summary: To analysis the miRNA expression profiles of PBMC from Normal Heatlh and Tuberculosis Patients

overall_design: 3 Healthy Donors vs 3 Tuberculosis Patients


title: Transcriptome Profiling of PanIN Cells Exposed to Tobacco Carcinogen

city: Miami

first: Nagaraj

last: Nagathihalli

state: Florida

address: 1550 NW 10th Ave

department: Surgery

institute: University of Miami

summary: Purpose: The goals of this study are to compare transcriptome profiling (RNA-seq) in pancreatic intraepithelial neoplasm (PanIN) cells exposed to tobacco-specific nitrosamine 4-(methyl nitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and to examine the upregulated pathways.

overall_design: Methods: Total RNA was isolated from PanIN cells treated with tobacco specific nitrosamine 4-(methyl nitrosamino)-1-(3-pyridyl)-1-butanone (NNK) for 5 and 50 days. Samples were processed for RNA-seq using standard methods on the Illumina HiSeq 2000 platform. Sequencing was performed in two multiplexed lanes of 100-bp single-end sequencing, which resulted in 75 million mappable reads per lane. The Illumina pipeline was used for base calling and quality filtering of sequence reads. Transcript assembly and abundance estimates of transcripts in fragments per kilobase of exon per million fragments mapped (FPKM) were performed by Cufflinks. Significant differences in total gene and transcript expression, splice site, transcription start site (TSS) and promoter usage were determined using a false discovery rate (FDR)-adjusted P-value. This study provides a framework for understanding transcriptional changes when pancreas cells exposed to tobacco specific nitrosamine.


title: Refined RIP-seq protocol for epitranscriptome analysis with low input materials

city: Toronto

first: Housheng

middle: Hansen

last: He

state: ON

address: 101 College St

institute: UHN

summary: We optimized the key parameters of m6A MeRIP-seq, including the starting amount of RNA, RNA fragmentation, antibody selection, MeRIP washing/elution conditions, methods for RNA library construction and the bioinformatics analysis pipeline. With the optimized immunoprecipitation conditions and a post-amplification rRNA depletion strategy, we were able to profile the m6A epitranscriptome using 2 µg of total RNA. We identified ~12,000 m6A peaks with a high signal/noise ratio from two lung adenocarcinoma (ADC) patient tumors. Through integrative analysis of the transcriptome, m6A epitranscriptome and proteome data in the same patient tumors, we identified dynamics at the m6A level that accounts for the discordance between mRNA and protein levels in these tumors.

overall_design: Refining MeRIP-seq by comparing 3 antibodies and 5 different amounts of staring materials in A549 cells line, in which 0.5ug library is with 2  replicates. Refined MeRIP-seq were applied to 2 lung Adenocarcinoma patient tumors

first: Shiyan

last: Wang

first: Yong

last: Zeng


title: Defective transcription elongation in a subset of cancers confers immunotherapy resistance (B16 ChIP-Seq)

first: Kakajan

last: Komurov

overall_design: RNA pol2 chipseq was perforemed on B16-F10 control and flavopiridol(25nM for 1 week) treated cell lines to access the impact of chronic inhibition of RNA pol2 elongation inhibition in its genome wide distribution.

first: Vishnu

last: Modur

first: Navneet

last: Singh

first: Vakul

last: Mohanty

first: Eunah

last: Chung

first: Belal

last: Muhammad

first: Kwangmin

last: Chen


title: mRNA-seq of bypass grafts in mice, utilizing the vena cava  as carotid artery bypass graft

city: vienna

first: Peter

last: Petzelbauer

address: Währinger Gürtel

department: Dermatology

country: Austria

institute: Medical University Vienna

summary: Surgical interventions on blood vessels bear a risk for intimal hyperplasia and atherosclerosis as a consequence of injury. A specific feature of intimal hyperplasia is the loss of vascular smooth muscle cell (VSMC) differentiation gene expression. We hypothesized that immediate responses following injury induce vascular remodeling. To differentiate injury due to trauma, reperfusion and pressure changes we analyzed vascular responses to carotid artery bypass grafting in mice compared to transient ligation. As a control, the carotid artery was surgically laid open only. In both, bypass or ligation models, the inflammatory responses were transient, peaking after 6h, whereas the loss of VSMC differentiation gene expression persisted. Extended time kinetics showed that transient carotid artery ligation was sufficient to induce a persistent VSMC phenotype change throughout 28 days. Transient arterial ligation in ApoE knockout mice resulted in atherosclerosis in the transiently ligated vascular segment but not on the not-ligated contralateral side. The VSMC phenotype change could not be prevented by anti-TNF antibodies, Sorafenib, Cytosporone B or N-acetylcysteine treatment. Surgical interventions involving hypoxia/reperfusion are sufficient to induce VSMC phenotype changes and vascular remodeling. In situations of a perturbed lipid metabolism this bears the risk to precipitate atherosclerosis.

overall_design: Comparison of mRNA changes between control tissue and bypass grafts perfused for 1, 6 and 24h. Number of replicated per group =4-5

first: Richard

last: Finsterwalder

first: Minu

last: Ganesan

first: Heide

last: Leb

first: Andreas

last: Habertheuer

first: José

last: Basílio

first: Irene

last: Lang

first: Milica

last: Krunic

first: Dominik

last: Wiedemann


title: Expression data from Tsc2-null cell line ELT3, and the ELT3-derivative rapamycin-resistant cell line ELT3-245

city: Memphis

first: Aristotelis

last: Astrinidis

state: TN

address: 50 N Dunlap

department: Pediatrics

institute: University of Tennessee Health Sciences Center

summary: Tuberous Sclerosis Complex (TSC) and Lymphangioleiomyomatosis (LAM) are caused by inactivating mutations in TSC1 or TSC2, leading to mTORC1 hyperactivation. The mTORC1 inhibitors rapamycin and analogs (rapalogs) are approved for treating of TSC and LAM. Due to their cytostatic and not cytocidal action, discontinuation of treatment leads to tumor regrowth and decline in pulmonary function. Therefore, life-long rapalog treatment is proposed for the control of TSC and LAM lesions, which increases the chances for the development of acquired drug resistance. Understanding the signaling perturbations leading to rapalog resistance is critical for the development of better therapeutic strategies. We developed the first Tsc2-null rapamycin-resistant cell line, ELT3-245, which is highly tumorigenic in mice, and refractory to rapamycin treatment. In vitro ELT3-245 cells exhibit enhanced anchorage-independent cell survival, resistance to anoikis, and loss of epithelial markers. A key alteration in ELT3-245 is increased β-catenin signaling. We propose that a subset of cells in TSC and LAM lesions have additional signaling aberrations, thus possess the potential to become resistant to rapalogs. Alternatively, when challenged with rapalogs TSC-null cells are reprogrammed to express mesenchymal-like markers. These signaling changes could be further exploited to induce clinically-relevant long-term remissions.

overall_design: Two cell lines (ELT3 and ELT3-245) were analyzed for global gene expression under no treatment (DMSO) and under treatment (20 nM rapamycin for 24 hours) conditions. All samples are in triplicate.

first: Matthildi

last: Valianou

first: Daniel

last: Johnson

first: John

last: Bissler


title: A Trio Based Approach to Epilepsy Methylome

city: Istanbul

first: ozkan

last: ozdemir

address: Kayisdagi Cad. No:32

department: Research and Development

country: Turkey

institute: Acibadem Labmed AŞ.

summary: Genome-wide methylation profiling on 15 Father-Mother-Offspring trios with Genetic Generalized Epilepsies. All trios have 2 affected (1 parent and offspring) and 1 healthy individuals. Illumina HumanMethylation450 BeadChip was used to obtain DNA methylation profiles which has probes for aproximetely 450000 CpG loci.

overall_design: Bisulphite converted DNA from the 45 samples (15 trios) were hybridised to the Illumina HumanMethylation450 BeadChip

first: Ozkan

last: Ozdemir

first: Ugur

last: Ozbek

first: Sibel Ugur

last: Iseri

first: Osman Ugur

last: Sezerman


first: Feng

last: Liu

summary: The C57B/6 mice were infected with Mtb H37Rv (CFU=200) for 28 days, and the miRNA expression profile from lung tissues were analyzed with deep sequencing.

overall_design: miRNA profiles of lung tissues from Mtb H37Rv infected C57B/6 mice and uninfected controls were generated by deep sequencing, in triplicate.

first: Baoxue

last: Ge


title: LSD1 regulates the plasmablast transcriptome

city: Atlanta

first: Jeremy

middle: Matthew

last: Boss

state: Georgia

address: 1510 Clifton Rd NE, Room 3120

department: Microbiology and Immunology

institute: Emory University

summary: To understand the role of LSD1 in B cell differentiation, mice with B cell conditional deletion of LSD1 were intravenously inoculated with LPS. After 3 days, B220+GL7-CD138- naïve B cells and CD138+ plasmablasts were FACS-sorted from the spleens and RNA-seq was performed to identify LSD1-target regulated genes.

overall_design: RNA-seq on control or LSD1-deficient murine naïve B cells or plasmablasts.

first: R

last: Haines

first: C

last: Scharer

first: J


title: Rhesus iPSC-CMs response to anoxia, comparing with human iPSC-CMs

city: Stanford

first: Lei

last: Tian

state: CA

address: 1215 Welch Rd

institute: Stanford's Postdoctoral Scholar programs

summary: RNA-Seq to compare hypoxia responses between human and rhesus macaque iPSC-CMs

sample_organism:
Macaca mulatta
Homo sapiens

platform_organism:
Macaca mulatta
Homo sapiens

overall_design: Both rhesus and human iPSC-Cardiomyocytes were subjected to anoxia condition, followed by RNA-Seq

first: Xin

last: Zhao

first: Haodong

last: Chen


title: Expression analysis of PC3 cells treated with scramble AON or AON directed against MBNL1

city: Singapore

first: Diana

middle: HP

last: Low

address: #03-06, 61 Biopolis Drive, Proteos

country: Singapore

institute: Institute of Molecular and Cell Biology

summary: We transfected PC3 cells with 100nM of a scrambled antisense oligonucleotide (AON) and an AON directed against MBNL1 exon 7 (36 basepairs) in order to skip the latter. Cells were harvested at 72h post-transfection and RNAseq was performed with ribozero depletion.

overall_design: For RNA-Seq library preparation we followed the Illumina TruSeq RNA Sample Preparation Kit v2 manual. At least 70 million, 75bp long paired end reads were mapped to the GRCh37/hg19 version of the human genome per replicate using STAR 2.4.2a (doi: 10.1093/bioinformatics/bts635) using the default parameters.

first: Tommaso

last: TABAGLIO

first: Heike

last: WOLLMANN

last: LOW

first: Pierre

last: GOY


title: LSD1 regulates plasmablast chromatin accessibility

summary: To understand the role of LSD1 in B cell differentiation, mice with B cell conditional deletion of LSD1 were intravenously inoculated with LPS. After 3 days, B220+GL7-CD138- naïve B cells and CD138+ plasmablasts were FACS-sorted from the spleens and RNA-seq was performed to identify LSD1-target regulated chromatin.

overall_design: ATAC-seq on control or LSD1-deficient murine naïve B cells or plasmablasts.

middle: M


title: LSD1 regulates plasmablast chromatin accessibility and transcriptome

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

overall_design: Refer to individual Series


title: Transcriptional analysis of PPARgamma activation in control and PPARgamma null macrophages

city: Philadelphia

first: Hoang

last: Nguyen

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania Perelman School of Medicine


title: Transcriptional analysis of PPARgamma activation in control and PPARgamma null macrophages [GRO-seq]

summary: The nuclear receptor Peroxisome Proliferator Activated Receptor gamma (PPARgamma) is known to regulate lipid metabolism in many tissues, including macrophages. Here we report that macrophage respiration is enhanced by rosiglitazone, an activating PPARgamma ligand, in a PPARgamma dependent manner. Moreover, PPARgamma is required for macrophage respiration even in the absence of exogenous ligand. Unexpectedly, the absence of PPARgamma dramatically affects the oxidation of glutamine. Both glutamine and PPARgamma have been implicated in alternative activation (AA) of macrophages and PPARgamma was required for IL4-dependent gene expression and stimulation of macrophage respiration. Remarkably, depletion of PPARgamma phenocopied the effects of glutamine depletion on transcription. Thus, PPARgamma supports alternative activation by facilitating glutamine metabolism. Yet PPARgamma expression is itself markedly increased by IL4. Thus, PPARgamma functions at the center of a feed forward loop that is central to AA of macrophages.

overall_design: Nascent RNA profiling of thioglycollate elicited macrophages untreated macrophages or macrophages treated for 24 hours with either DMSO or Rosiglitazone

first: Victoria

last: Nelson

middle: C

first: Erika

last: Briggs

first: Wesley

middle: Y

last: Ho

first: Joanna

last: Dispirito

first: Jill

last: Maranis

first: David

middle: A

last: Hill

first: Mitchell

last: Lazar


title: Animal model of acute-on-chronic alcoholic liver injury

status: Public on Sep 05 2018

city: College Station

first: Ivan

last: Rusyn

state: TX

address: 4458 TAMU

institute: TEXAS A&M UNIVERSITY

summary:
Background and aims: We aimed to study the pathogenesis of AH in an animal model of acute-on-chronic alcoholic liver disease which combines chronic hepatic fibrosis with intragastric alcohol administration.
Methods: Adult male C57BL6/J mice were treated with CCl4 (0.2 ml/kg, 2×weekly by intraperitoneal injections for 6 weeks) to induce chronic liver fibrosis. Then, ethyl alcohol (EtOH) (up to 25 g/kg/day, for 3 weeks) was administered continuously to mice via a gastric feeding tube, with or without one-half dose of CCl4. Liver and serum markers were evaluated to characterize acute-on-chronic-alcoholic liver disease in our model.
Results: CCl4 or EtOH treatment alone induced liver fibrosis or steatohepatitis, respectively, findings that were consistent with expected pathology. Combined treatment with CCl4 and EtOH resulted in a marked exacerbation of liver injury, as evident by the development of hepatic inflammation, marked steatosis, and pericellular fibrosis, and by increased serum transaminase levels, compared to mice treated with either treatment alone. Liver transcriptomic changes specific to combined treatment group demonstrated close concordance with pathways perturbed in human severe cases of AH. In addition to gene expression changes, E. coli and Candida species were also significantly more abundant in livers of mice co-treated with CCl4 and EtOH.
Conclusions: Mice treated with CCl4 and EtOH displayed several key characteristics of human AH, including pericellular fibrosis, increased hepatic bacterial load, and dysregulation of the same molecular pathways. This model may be useful for developing therapeutics for AH.

first: Rusyn

last: Ivan

first: Shinji

last: Furuya

first: Hisataka

last: Fukushima


title: Maternal Diet Enriched with Alpha Linolenic or Saturated Fatty Acids Differentially Regulates Gene Expression in Mice Offspring's liver.

city: Tel Aviv

first: Metsada

last: Pasmanik-Chor

address: Ramat Aviv

department: Biology

country: Israel

institute: Tel Aviv University

summary: Lipid metabolic disarray in young and adult mice offspring's liver is induced by saturated fatty acids (SFA) but prevented by alpha linolenic acid (ALA, 18:3 ω3) in the maternal diet during pregnancy and lactation. The aim of the present study was to analyse the impact of maternal dietary ALA on the liver gene expression in the new-born offspring in comparison to a SFA diet. Methods: C57Bl6/J dams were fed with diets normal in calories but rich in ALA or SFA before mating and during pregnancy. Pups were sacrificed at birth and liver parameters were assessed. Gene expression was characterized by microarray analysis and validated by real time qPCR. Results: ALA compared to SFA in maternal diets during pregnancy, increased polyunsaturated fatty acids while differentially modified fatty acid desaturase activities in offspring liver. Overall, 474 and 662 genes from born pups’ liver, were differentially regulated by ALA and SFA compared to control diet (p<0.05; Fold change 2), respectively. Notably, Per3 was up-regulated by ALA whereas down-regulated by SFA, compared to control diet. Conclusions: ALA and SFA enriched diets differentially affect gene expression pattern in the offspring’s liver. ALA in particular, upregulates genes associated to low adiposity.

overall_design: Effect of maternal diet on mice offspring liver gene expression.

first: Alicia

last: Leikin Frenkel

first: Limor

last: Shomonov-Wagner

first: Ana

last: Juknat


title: Transcriptional analysis of PPARgamma activation in control and PPARgamma null macrophages [ChIP-seq]

overall_design: Immuno-precipitation followed by high throughput sequencing of thioglycollate elicited macrophages harvested from four control and four PPARgammaKO mice.


title: LaminA/C regulates epigenetic and chromatin architecture changes upon aging of hematopoietic stem cells

city: Ulm

first: Medhanie

middle: Assmelash

last: Mulaw

address: Albert-Einstein-Allee 11

country: Germany

institute: University of Ulm

summary: The decline of hematopoietic stem cell (HSC) function upon aging contributes to the senescent immune remodeling and to leukemia pathogenesis. Aged HSCs show changes in their epigenome, like alterations in the global and local DNA/histone methylation and histone acetylation landscape. Previously, we showed a correlation between high Cdc42 activity and the loss of intra-nuclear epigenetic polarity (epipolarity), as indicated by the specific location of histone H4 lysine 16 acetylation (H4K16ac). Here, we show that not all histone modifications display a polar localization and that loss of H4K16ac amount and epipolarity is specific to aged HSCs. Increased levels of H4K16ac are insufficient to restore polarity in aged HSCs and for the restoration of HSC function. Changes in H4K16ac upon aging and rejuvenation of HSCs are correlated to a shift of chromosome 11 architecture and nuclear volume and shape. Surprisingly, by taking advantage of knock-out mouse models we demonstrate that increased Cdc42 activity levels correlate with the repression of LaminA/C expression, which control chromosome 11 distribution, H4K16ac polarity and the nuclear volume and shape of aged HSCs. These chromatin and epigenetic architecture changes are targeted by altering the activity of the small RhoGTPase Cdc42, that regulates LaminA/C. Collectively, our data show that chromatin architecture changes in stem cells are reversible by changing levels of Cdc42 activity, revealing an unanticipated way to pharmacologically target LaminA/C expression and revert alterations of the epigenetic architecture in aged HSCs.

overall_design: HSC (>= 200 cells) were first sorted from Young (2-4-month-old) and aged (20-26-month-old; ± CASIN) C57BL/6 mice (>= 3 individuals per experimental arm) and dropped into lysis buffer for subsequent RNA-seq library preparation.


title: Histone locus regulation by the Drosophila dosage compensation adaptor protein CLAMP

first: Matthew

last: Booker

address: 21-27 Burlington Ave.

department: Informatics

institute: Dana Farber Cancer Institute

summary: The conserved histone locus body (HLB) assembles prior to zygotic gene activation early during development and concentrates factors into a nuclear domain of coordinated histone gene regulation. Although HLBs form specifically at replication-dependent histone loci, the cis and trans factors that target HLB components to histone genes remained unknown. Here we report that conserved GA repeat cis elements within the bidirectional histone3-histone4 promoter direct HLB formation in Drosophila In addition, the CLAMP (chromatin-linked adaptor for male-specific lethal [MSL] proteins) zinc finger protein binds these GA repeat motifs, increases chromatin accessibility, enhances histone gene transcription, and promotes HLB formation. We demonstrated previously that CLAMP also promotes the formation of another domain of coordinated gene regulation: the dosage-compensated male X chromosome. Therefore, CLAMP binding to GA repeat motifs promotes the formation of two distinct domains of coordinated gene activation located at different places in the genome.

overall_design: To map the occupancy of CLAMP at the histone locus during development, we performed CLAMP small-scale ChIP-seq on staged female-enriched embryo pools.

first: Leila

middle: E

last: Rieder


title: CROP-Seq in Primary Human T Cells

city: San Francisco

first: Eric

last: Shifrut

address: 513 Parnassus Ave, HSW 1033

institute: University of California, San Franscisco

summary: We adapted sgRNA lentiviral infection and Cas9 electroporation (SLICE) to allow for CROP-Seq (Datlinger et al, Nat Med 2017) in primary cells. We used a library of 48 sgRNA, derived from GW screens, to explore transcriptional changes downstream of CRISPR-KO.

overall_design: Pooled CRISPR screen with single cell RNASeq readout (Perturb-Seq / CROP-Seq) in primary human T cells. Dataset includes CD8 T cells from two donors, for two conditions: with TCR stimulation or No stimulation.

first: Julia

last: Carnevale

first: Alexander

last: Marson


title: Comprehensive molecular characterization of microneedling therapy in a human three-dimensional skin model

city: Aachen

first: Sebastian

last: Huth

address: Pauwelsstr. 30

institute: Uniklinik RWTH Aachen

summary: We present for the first time the direct molecular effects of microneedling therapy on epidermal keratinocytes and dermal fibroblasts using a standardized 3D skin model. Microneedling treatment resulted in histological alterations and changed the expression of various genes related to epidermal differentiation, inflammation, and dermal remodeling. We speculate that skin microneedling plays a role in dermal remodeling, increases epidermal differentiation, and might also have a direct effect on collagen synthesis. These findings may increase our understanding of the molecular mechanisms of human skin repair induced by microneedling therapy and will allow comparisons with competing applications, such as laser therapies

overall_design: Six samples were analyzed: Comparison between 3D skin models after microneedling treatment (n=3)  vs. untreated controls (n=3).

first: Laurenz

last: Schmitt

first: Yvonne

last: Marquardt

first: Philipp

last: Amann

first: Ruth

last: Heise

first: Laura

first: Sylvia

last: Wagner-Schiffler

first: Jens

last: Baron


title: Expression data from hyperthermia- and/or radiation-treated A549 lung cancer cells

city: Busan

first: Beomseok

last: Son

address: 322 Biology Building, 2 Busandaehakro 63beon-gil, Geumjeong-gu

country: South Korea

institute: Pusan National University

summary:
Lung cancer is one of the leading incident cancers among the various cancer types that occur in human. About 85% of lung cancer is non-small cell lung cancer (NSCLC). NSCLC is often diagnosed at the advanced stage and metastasis occurs in most cases, which explains why the overall survival rates for NSCLC are still low. Hyperthermia (HT) is one of the promising therapies in combination with chemotherapy and radiotherapy, and is known to be effective in improving survival and quality of life in patients with advanced lung cancer.
We used microarrays to detail the global program of gene expression underlying HT and ionizing radiation (IR) combination therapy and identified a variety of genes whose expressions were regulated during this process.

overall_design: HT- or IR-treated A549 cells were included in the study. There is a control group. Six samples were analyzed and each group does not have replicates.

first: Jaewan

last: Jeon

first: Sungmin

last: Lee

first: BuHyun

last: Youn


title: Genome-wide binding of condensin II and TFIIIC in human HEK293 cells

city: Kansas City

first: Jennifer

last: Gerton

state: Missouri

address: 1000 E. 50th Street

institute: Stowers Institute for Medical Research

summary: Condensin complexes are highly conserved for chromosome compaction to ensure their faithful segregation in mitosis. However, little is known about the role of condensin complexes in interphase. Condensins exists in two complexes, condensins I and II, in higher eukayotic cells. During interphase, condensin II is predominantly localized in the nucleus throughout the cell cycle, whereas condensin I is localized at the cytoplasm in interphase. The distinct localization patterns suggest that condensin II, but not condensin I, may contribute to genome organization in interphase. Our results suggest that condensin II is associated with TFIIIC complex in humans.

overall_design: Examination of binding of condensin II and TFIIIC complexes in HEK293 cells by ChIPseq

first: K

last: Yuen

first: J

middle: L


title: Global analysis of microRNA target sites in human osteoblasts

city: Seoul

first: Young-Soo

last: Kwon

address: Nungdongro 209, Gwangjingu

department: Department of Bioscience and Biotechnology

institute: Sejong University

summary: In this study, we determined target sites of microRNA in human osteoblasts by using CLIP-seq for endogenous AG02. Our results suggest a novel mechanism of tumorigenesis by oncomiRs from the miR17~92 cluster through post-transcriptional repression of RNA degradation pathways.

overall_design: CLIP-seq of endogenous AGO2 by using anti-AGO2-antibody (Proteintech) and IgG controls


title: H3K4me1 ChIP-seq analysis in Jurkat cells

city: Lund

first: Phuong

last: Cao Thi Ngoc

address: BMC, B1222b, Klinikgatan 26

country: Sweden

institute: Lund University

summary: ChIP-seq analysis was performed in Jurkat cells (T-cell acute lymphoblastic leukemia cell line)

overall_design: H3K4me1 ChIP-seq

first: Lee

last: Lawton

first: Tze

middle: K

last: Tan

first: Takaomi

last: Sanda


title: ATAC-seq data

city: Seattle

first: Diego

last: Calderon

address: 3720 15th Ave NE

institute: University of Washington

summary: The immune system depends on a balanced interplay among a variety of specialized cell types transitioning between resting and stimulated states. While epigenome mapping efforts have focused on resting ex vivo immune cells, efforts to characterize stimulation-induced chromatin changes of diverse cell types has been limited. Thus, we collected ATAC-seq and RNA-seq data from immune cell types under resting and stimulated conditions from blood of healthy individuals, and cell types from fetal thymus samples.

overall_design: 175 ATAC-seq samples of 25 blood cell types from healthy donors.

first: Michelle

last: Nguyen

first: Anja

last: Mezger


title: FFPE samples profiled on HG-U133plus2 array with  Affymetrix's GeneChip® 3' IVT Express kit

city: Brussels

first: Vinu

last: Jose

address: Rue Meylemeersch 90

institute: Institut Jules Bordet – Université Libre de Bruxelles (ULB)

summary: The reliability of differential expression analysis on FFPE expression profiles from Affymetrix arrays is questionable, due to the wide range of percent-present values reported in studies which profiled FFPE samples on Affymetrix arrays. Moreover the validity of externally defined gene-modules in FFPE microarray expression profiles is unknown. Using eight breast cancer tumors with available frozen and FFPE samples, five sample-matched data sets were generated from different combination of Affymetrix arrays, amplification-and-labeling kit and sample preservation method.  The reliability of differential expression analysis was investigated by developing de novo ER/HER2 pathway gene-modules from matched data sets and validating it on external data set using ROC analysis. Spearman's rank correlation coefficient of module scores between matched FFPE-frozen expression profiles was used to measure reliability of externally defined gene-modules in FFPE expression profiles. Independent of array/amplification-kit/sample preservation method used, de novo ER/HER2 gene-modules derived from all matching data sets showed similar prediction performance during independent validation (AUC range; ER: 0.92-0.95, HER2: 0.88-0.91), except for de novo HER2 gene-module derived from FFPE data set with 3'IVT kit (AUC: 0.67-0.72). Further not all gene-module based biological signals present in frozen expression profiles can be recovered from matching FFPE microarray expression profiles using the currently available FFPE specific sample preparation kits. The gene-module based biological signal extracted from FFPE RNA, using microarrays, may not be as reliable as that from their frozen counterpart, if the sample preparation protocol used with FFPE RNA failed to recover relevant genes involved in the biological signal.

overall_design: RNA were extracted from eight FFPE preserved breast cancers. RNAs were amplified and labeled using Affymetrix's GeneChip® 3' IVT Express kit, and profiled on Affymetrix's GeneChip® HG-U133 Plus2.0 Array according to Affymetrix's standard procedure.

first: Debora

last: Fumagalli

first: Françoise

last: Rothé

first: Samira

last: Majjaj

first: Sherene

last: Loi

first: Stefan

last: Michiels

first: Christos

last: Sotiriou


title: FFPE samples profiled on HG-U219 array with Nugen's Ovation® FFPE WTA System and EncoreTM Biotin Module

overall_design: RNAs were extracted from eight FFPE preserved breast cancers. RNAs were amplified and labeled using Nugen's Ovation® FFPE WTA System and EncoreTM Biotin Module, and profiled on Affymetrix® HG-U219 Array Plate according to Affymetrix's standard procedure.


title: Fresh-Frozen samples profiled on HG-U133plus2 array with Affymetrix's GeneChip® 3' IVT Express kit

overall_design: RNAs were extracted from eight Fresh-Frozen preserved breast cancers. RNAs were amplified and labeled using Affymetrix's GeneChip® 3' IVT Express kit, and profiled on Affymetrix's GeneChip® HG-U133 Plus2.0 Array according to Affymetrix's standard procedure.


title: FFPE samples profiled on HG-U219 array with Affymetrix's SensationPlusTM FFPE Amplification and 3'IVT Labeling kit

overall_design: RNAs were extracted from eight FFPE preserved breast cancers. RNAs were amplified and labeled using Affymetrix's SensationPlusTM FFPE Amplification and 3'IVT Labeling kit, and profiled on Affymetrix® HG-U219 Array Plate according to Affymetrix's standard procedure.


title: Recovery and analysis of transcriptome subsets from pooled single-cell RNA-seq libraries

status: Public on Sep 04 2018

city: Aurora

first: Kent

middle: Augustus

last: Riemondy

state: Colorado

department: Biochemistry and Molecular Genetics

institute: University of Colorado School of Medicine

summary: Single-cell RNA sequencing (scRNA-seq) methods generate sparse gene expression profiles for thousands of single cells in a single experiment. The information in these profiles is sufficient to classify cell types by distinct expression patterns but the high complexity of scRNA-seq libraries prevents full characterization of transcriptomes from individual cells. To generate more focused gene expression information from scRNA-seq libraries, we developed a strategy to physically recover the DNA molecules comprising transcriptome subsets, enabling deeper interrogation of the isolated molecules by another round of DNA sequencing. We applied the method in both a cell-centric and gene-centric mode to isolate mRNA fragments from scRNA-seq libraries.

overall_design: targeted resequencing and original untargeted datasets of various scRNA-Seq libraries from the 10x genomics and wafergen platform

first: Jay

middle: R

last: Hesselberth


title: Expression data from knockdown of Tyro3 in hepatocellular carcinoma

city: 台北市

first: 佳良

last: 蔡

state: TWN

address: 復興北路486號

country: Taiwan

institute: Chang Gung Memorial Hospital

summary: Tyro3 is a member of the TAM (Tyro3, Axl and Mer) receptor family. In this study, we want to know potential association between Tyro3 expression in HCC and the involved signaling pathway.

overall_design: We used siRNA to knock down Tyro3 in Huh7 cells. And expressed this proflie by array.

first: Sen-Yung

last: Hsieh

first: Chia-Liang

last: Tsai


title: Human Adipocytes Regulate Gene Expression in Triple-negative Breast Cancer Assessed by NGS  Sequencing

city: Shanghai

first: Zhonghua

last: Tao

state: Shanghai

address: No.270, Dong'an Road, Xuhui.

institute: Fudan University Shanghai Cancer Center

summary: Adipocyte was found play a pivotal role in tumorgenesis, progression and metastasis in breast cancer. However, affection of adipocyte on gene expression profile in triple-negative breast cancer (TNBC) is still not clear. In the present study, firstly we reported the gene expression profiles of TNBC regulated by human adipocytes using NGS. TNBC cell MDA-MB-231 was used in this study. MDA-MB-231 cells were treated with medium derived from adipocytes culture supernatants. Using two different RNA libraries, we sequenced the complete transcriptome(including mRNA, lncRNA, circleRNA and small RNA) of MDA-MB-231 treated with medium derived from adipocytes culture supernatants.

overall_design: NGS sequencing of wild type and adipocyte treated MDA-MB-231 cells, and identifing differentiated expressed genes


title: Effect of TGF-beta treatment on circRNAs biogenesis

city: Houston

first: yu

last: xiang

state: Texas

address: 6431 Fannin

institute: UTHealth McGovern Medical School

summary: circRNAs profile were examined upon TGF-beta treatment in A549 cells

overall_design: Examination of circRNAs profile in TGF-beta treated and TGF-beta+ SIS3 inhibitor group

first: Leng

last: Han

first: Yu

last: Xiang


title: Feasibility of Developing Reliable Gene Expression Modules from FFPE Derived RNA Profiled on Affymetrix Arrays

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

The reliability of differential expression analysis on FFPE expression profiles from Affymetrix arrays is questionable, due to the wide range of percent-present values reported in studies which profiled FFPE samples on Affymetrix arrays. Moreover the validity of externally defined gene-modules in FFPE microarray expression profiles is unknown. Using eight breast cancer tumors with available frozen and FFPE samples, five sample-matched data sets were generated from different combination of Affymetrix arrays, amplification-and-labeling kit and sample preservation method.  The reliability of differential expression analysis was investigated by developing de novo ER/HER2 pathway gene-modules from matched data sets and validating it on external data set using ROC analysis. Spearman's rank correlation coefficient of module scores between matched FFPE-frozen expression profiles was used to measure reliability of externally defined gene-modules in FFPE expression profiles. Independent of array/amplification-kit/sample preservation method used, de novo ER/HER2 gene-modules derived from all matching data sets showed similar prediction performance during independent validation (AUC range; ER: 0.92-0.95, HER2: 0.88-0.91), except for de novo HER2 gene-module derived from FFPE data set with 3'IVT kit (AUC: 0.67-0.72). Further not all gene-module based biological signals present in frozen expression profiles can be recovered from matching FFPE microarray expression profiles using the currently available FFPE specific sample preparation kits. The gene-module based biological signal extracted from FFPE RNA, using microarrays, may not be as reliable as that from their frozen counterpart, if the sample preparation protocol used with FFPE RNA failed to recover relevant genes involved in the biological signal.

overall_design:
Refer to individual Series

Using eight breast cancer tumors with available frozen and FFPE samples, five sample-matched data sets were generated from different combination of arrays , amplification-and-labeling kit and sample preservation method as listed below; 1) Two data set from matched FFPE and frozen samples profiled on HG-U133plus2 arrays with Affymetrix's 3'IVT kit (u133p2.3ivt array / 3ivt kit), 2) Two data set from matched FFPE and frozen samples profiled on HG-U219 arrays with Nugen's Ovation® FFPE WTA System and EncoreTM Biotin Module (u219.ovation arrays / ovation kit), and 3) a single data set from matched FFPE samples profiled on HG-U219 arrays with Affymetrix's SensationPlusTM FFPE Amplification and 3'IVT Labeling Kit (u219.sensation array / sensation kit). We consider the data set which profiled frozen samples on HG-U133plus2 array with 3'IVT kit as 100% truth and compared all other data sets to this reference data set. The eight BC tumors include two tumors from each Luminal-A, Luminal-B, HER2-amplified and Triple-Negative subtypes


title: Mechanism suppressing H3K9 trimethylation in pluripotent stem cells and its demise by polyQ-expanded huntingtin mutations [ChIP-seq]

city: Cologne

first: David

last: Vilchez

state: NRW

address: Joseph Stelzmann Strasse, 26

institute: CECAD - Cluster of Excellence

summary: We find that HTT binds ATF7IP, a regulator of the histone H3 methyltransferase SETDB1. HTT inhibits the interaction of the ATF7IP-SETDB1 complex with other heterochromatin regulators and transcriptional repressors, maintaining low levels of H3K9 trimethylation (H3K9me3) in hESCs. Conversely, loss of HTT promotes global increased H3K9me3 levels. To test whether HTT knockdown also induces enrichment of H3K9me3 marks at specific genes, we performed chromatin immunoprecipitation (ChIP)-sequencing assays of hESCs using an antibody to H3K9me3.

overall_design: We performed chromatin immunoprecipitation (ChIP)-sequencing using H3K9me3 antibody (Abcam, #8898, reported suitable for ChIP) comparing H9 hESCs expressing non-targeting (NT) shRNA with H9 hESCs expressing HTT shRNA. Two biological replicates from independent experiments were analyzed.

first: Dilber

last: Irmak

first: Azra

last: Fatima

first: Ricardo

last: Gutiérrez-Garcia

first: Markus

last: Rinschen

first: Prerana

last: Wagle

first: Janine

last: Altmüller

first: Barbara

last: Hummel

first: Corinna

last: Klein

first: Christian

last: Frese

first: Ritwick

last: Sawarkar

first: Alvaro

last: Rada-Iglesias


title: Mechanism suppressing H3K9 trimethylation in pluripotent stem cells and its demise by polyQ-expanded huntingtin mutations [RNA-seq]

overall_design: We performed RNAseq in pluripotent stem cells and derived NPCs to examine how changes in HTT and ATF7IP levels change transcript levels. We have 19 samples in total:  3 replicate NPCs derived from HD iPSCs expressing Nt shRNA +  3 NPCs derived from HD iPSCs expressing ATF7IP  shRNA  to be compared with 3 NPCs derived from Control iPSCs expressing Nt shRNA; 2 replicates H9 hESCs expressing ATF7IP  shRNA to be compared with 2 replicates H9 hESCs expressing control NT shRNA; 3 replicates NPCs derived from H9 hESCs expressing HTT  shRNA to be compared with  3 replicates NPCs derived from H9 hESCs expressing control NT  shRNA


title: Transcriptional analysis of PPARgamma activation in control and PPARgamma null macrophages [RNA-seq]

city: Philadelphia

first: Hoang

last: Nguyen

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania Perelman School of Medicine

summary: The nuclear receptor Peroxisome Proliferator Activated Receptor gamma (PPARgamma) is known to regulate lipid metabolism in many tissues, including macrophages. Here we report that macrophage respiration is enhanced by rosiglitazone, an activating PPARgamma ligand, in a PPARgamma dependent manner. Moreover, PPARgamma is required for macrophage respiration even in the absence of exogenous ligand. Unexpectedly, the absence of PPARgamma dramatically affects the oxidation of glutamine. Both glutamine and PPARgamma have been implicated in alternative activation (AA) of macrophages and PPARgamma was required for IL4-dependent gene expression and stimulation of macrophage respiration. Remarkably, depletion of PPARgamma phenocopied the effects of glutamine depletion on transcription. Thus, PPARgamma supports alternative activation by facilitating glutamine metabolism. Yet PPARgamma expression is itself markedly increased by IL4. Thus, PPARgamma functions at the center of a feed forward loop that is central to AA of macrophages.

overall_design: RNA profiling of thioglycollate elicited macrophages harvested from four control and four PPARgammaKO mice. Untreated macrophages or macrophages treated for 24 hours with either DMSO, IL4, or Rosiglitazone

first: Victoria

last: Nelson

first: Erika

last: Briggs

first: Wesley

last: Ho

first: Joanna

last: Dispirito

first: Jill

last: Maranis

last: Hill

first: Mitchell

last: Lazar


title: MRI-informed muscle biopsies correlate MRI with pathology and DUX4 target gene expression in FSHD

first: Stephen

last: Tapscott

state: WASHINGTON

address: 1100 Fairview N. Ave

department: Human Biology

institute: Fred Hutch Cancer Research Center

summary: Facioscapulohumeral muscular dystrophy (FSHD) is a common, dominantly inherited disease caused by the epigenetic de-repression of the DUX4 gene, a transcription factor normally repressed in somatic cells. As targeted therapies are now possible in FSHD, a better understanding of the relationship between DUX4 activity, muscle pathology and muscle MRI changes are crucial both to understand disease mechanisms and for the design of future clinical trials. Here, we performed MRIs of the lower extremities in 36 individuals with FSHD, followed by needle muscle biopsies in safely accessible muscles. We examined the correlation between MRI characteristics, muscle pathology, and expression of DUX4 target genes. Results show that the presence of elevated MRI STIR signal has substantial predictive value in identifying muscles with active disease and DUX4 target gene expression. In addition, DUX4 target gene expression was detected only in FSHD-affected muscles and not in control muscles, and higher levels of DUX4 target expression was associated with more advanced muscle pathology. These results support the use of MRI to identify FSHD muscles with active disease as measured by histopathology and DUX4 target gene expression and might be useful for the design of studies of disease progression and response to intervention.

overall_design: Recruitment for the study included thirty-six subjects (34% female) with genetically confirmed FSHD (34 FSHD1, 2 FSHD2). RNA sequencing was performed on muscle biopsy samples from 34 of the 36 FSHD subjects, and on 9 control quadriceps muscle biopsies from unaffected individuals.

first: Seth

last: Freidman

first: Dennis

last: Shaw

first: Leo

last: Wang

first: Lauren

last: Snider

first: Chao-Jen

last: Wong

first: Chris

last: Budech

first: Nancy

last: Gove

first: Leann

last: Lewis

first: Amy

last: Campbell

first: Rabi

last: Tawil


title: Mechanism suppressing H3K9 trimethylation in pluripotent stem cells and its demise by polyQ-expanded huntingtin mutations

first: David

last: Vilchez

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

overall_design: Refer to individual Series


title: YAP-TEAD signaling promotes Basal Cell Carcinoma development via c-JUN/AP1 axis [ChIP-seq]

city: Torino

first: Raffaele

last: Calogero

state: To

address: Via Nizza 52

department: Molecular Biotechnology Center

institute: University of Torino

summary: The mammalian Hippo signaling pathway, through its effectors YAP and TAZ, coerces epithelial progenitor cell expansion for appropriate tissue development or regeneration upon damage.  Its ability to drive rapid tissue growth explains why many oncogenic events frequently exploit this pathway to promote cancer phenotypes.  Indeed, several tumor types including basal cell carcinoma (BCC) show genetic aberrations in the Hippo (or YAP/TAZ) regulators.  Here, we uncover that while YAP is dispensable for homeostatic epidermal regeneration, it is required for BCC development.  Our clonal analyses further demonstrate that few emerging Yap-null dysplasia have lower fitness and thus are diminished as they progress to invasive BCC.  Mechanistically, YAP depletion in BCC tumors leads to effective impairment of the JNK-JUN signaling, a well-established tumor driving cascade.  Importantly, in this context, YAP does not influence canonical Wnt or Hedgehog signaling.   Overall, we reveal the Hippo signaling as an independent promoter of BCC pathogenesis and thereby a viable target for drug-resistant BCC.

overall_design: YAP transcriptional function in BCC

first: Dejan

last: Maglic

first: Karin

last: Schlegelmilch

first: Antonella

middle: F

last: Dost

first: Riccardo

last: Panero

first: Michael

last: Dill

first: Fernando

middle: D

last: Camargo


title: YAP-TEAD signaling promotes Basal Cell Carcinoma development via c-JUN/AP1 axis


title: HNF1A is a Novel Oncogene and Central Regulator of Pancreatic Cancer Stem Cells

city: Ann Arbor

first: Mats

last: Ljungman

state: Michigan

address: NCRC, B520 Room 1346 2800 Plymouth Rd.

institute: University of Michigan