title: Gene Expression Patterns of Endothelial Cell Network Formation

city: Durham

first: Lisa

last: Satterwhite

state: North Carolina

address: 101 Science Drive

department: Department of Civil and Environmental Engineering

institute: Duke University

summary:
Lamellar co-cultures of human aorta-derived smooth muscle cells (SMCs) cultured with cord-blood derived endothelial cells (ECs) are an in vitro model for tissue engineered blood vessels and in-growth of endothelial cells into cardiovascular repair devices.
The ratio of endothelial cells to smooth muscle cells can control the EC pattern of growth and differentiation.  Low density ECs form capillary-like networks in co-culture with SMCs whereas high density ECs become confluent across the top surface of the SMCs.  To understand the molecular mechanisms that govern network formation, used microarray analysis of ECs purified from 1) networks, 2) confluent layers compared to 3) ECs in monoculture.

overall_design: To understand the molecular mechanisms that govern endothelial cell network formation, we used microarray analysis of RNA isolated from endothelial cells in either in monoculture or lamellar culture with smooth muscle cells.

first: Aswati

last: Avarind

first: Erica

last: Brown

first: George

last: Truskey


title: Methotrexate resistant cell lines for the study of gestational trophoblastic neoplasia

status: Public on Mar 03 2017

city: Boston

first: Kevin

middle: Meyer

last: Elias

state: MA

address: 75 Francis Street

department: OB/GYN

country: USA

institute: Brigham and Women's Hospital

summary:
The term gestational trophoblastic disease (GTD) describes a range of pathologies derived from the villous trophoblasts of the placenta.  These include benign entities such as partial and complete hydatidiform mole as well as invasive cancers such as gestational choriocarcinoma, placental site trophoblastic tumors, and epithelioid trophoblastic tumors. Collectively, the malignant forms of GTD are known as gestational trophoblastic neoplasia (GTN).    The risk of GTN following a complete molar pregnancy ranges between 8-25%. Low risk patients are expected to have a high likelihood of response to single agent chemotherapy with methotrexate or actinomycin D, but the incidence of resistance to single agent chemotherapy among low risk patients remains 25-50%.
We used gene expression microarrays to compare methotrexate sensitive trophoblastic cell lines to sublines that were conditioned to become methotrexate resistant.

overall_design: Two trophoblastic cell lines, CRL-1584 (3A-Sub E) and JEG-3 were purchased from American Type Culture collection (ATCC) (Manassas, VA).  CRL-1584 (3A-Sub E) was originally derived from human term primary placental cells and then immortalized using SV40 virus.   JEG-3 is a clonal human choriocarcinoma.  The cell lines were serially passaged in complete medium supplemented with each cell line’s respective IC50 concentration of methotrexate until the cell lines were able to proliferate normally.  Subsequently, the concentration of methotrexate was increased by one half-log concentration.  The process was repeated iteratively until the cells became senescent. At each log concentration of methotrexate resistance, cell line stocks were frozen to establish a separate subline of each cell line.  Based on their relative level of resistance to methotrexate, these were designated JEG-3-R7, JEG-3-R6, and JEG-3-R5 (for 10-7 M through 10-5 M methotrexate resistance).  Over the same time period (approximately 11 months), we were able to induce only one order of magnitude of resistance in the normal placenta cell line; that line was designated NP-R7.   In parallel, the parent cell lines were passaged in normal medium to control for any physiologic changes induced by prolonged culture in vitro.

middle: M


title: Expression data from CSF1- or CSF2-induced bone marrow derived macrophages (BMDMs): M(CSF1) and M(CSF2) cells.

status: Public on Feb 28 2017

city: shanghai

first: Jian-Yang

last: Ao

state: State...

address: fenglin 180#, Xuhui district,shanghai

country: China

institute: Fudan University

summary:
Femur and tibia bones were harvested from 8-week-old wild-type (WT) C57BL/6 mice. Bone marrow was flushed out into cold PBS (Life Technologies) plus 2% heat-inactivated FBS, passed through a needle five times to dissociate the cells, and then passed through a 70-μm cell strainer (Becton Dickinson) to remove cell clumps, bone, hair, and other cells/tissues. After addition of three volumes of NH4Cl solution (0.8% NH4Cl solution; Beyotime Institute of Biotechnology, Jiangsu, China), the mixture was incubated on ice for 10 min to remove red blood cells; the cells were then spun down and resuspended in cold PBS with 2% FBS. The harvested cells were cultured in DMEM containing 10% FBS and supplemented with 10 ng/ml recombinant mouse CSF1 (R&D Systems) or 10 ng/ml recombinant mouse CSF2 (R&D Systems) for 7 days to obtain CSF1- or CSF2-induced BMDMs: M(CSF1) or M(CSF2) cells, respectively. To test the difference genes expression of TAMs obtained from M(CSF1) and M(CSF2) cells in C57BL/6 mice.
We used microarrays to detail the global programme of gene expression and identified M(CSF1) and M(CSF2) cells during this process.

overall_design: To test the difference genes expression of M(CSF1) and M(CSF2) cells.M(CSF1) cells, M(CSF2) cells were processed in Trizol within 4 h after sorting and then analyzed using whole-mouse genome Affymetrix Mouse Gene 1.0 ST Arrays.

first: Hui-Chuan

last: Sun


title: Autophagy maintains metabolism and functional activity of a subset of aged hematopoietic stem cells [gene expression]

city: San Francisco

first: Emmanuelle

last: Passegue

state: CA

address: 35 Medical Center Way, RMB-1017, Box 0667

department: Department of Medicine, Hem/Onc Division

institute: The Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, University of California San Francisco

summary:
Autophagy is critical for protecting HSCs from metabolic stress. Here, we used a genetic approach to inactivate autophagy in adult HSCs by deleting the Atg12 gene. We show that loss of autophagy causes accumulation of mitochondria and an oxidative phosphorylation (OXPHOS)-activated metabolic state, which drives accelerated myeloid differentiation likely through epigenetic deregulations rather than transcriptional changes, and impairs HSC self-renewal activity and regenerative potential.
To determine how loss of autophagy affects gene expression, we conducted microarray analysis of purified control and Atg12 conditional knockout HSCs.

overall_design: Atg12flox/flox:Mx1-Cre conditional knockout mice and control Atg12flox/flox mice were injected with poly(I:C) at 4 week of age, and HSCs (Lin-/c-Kit+/Sca-1+/Flk2-/CD150+/CD48-) were isolated from the bone marrow of individual mice 2-3 months later. RNA was extracted, and microarray analysis was conducted with Affymetrix Gene ST 1.0 microarrays as described in the methods.

first: Theodore

middle: T

last: Ho

first: Matthew

middle: R

last: Warr

first: Emmalee

last: Adelman

first: Evgenia

middle: V

last: Verovskaya

first: Olivia

last: Lansinger

first: Johanna

last: Flach

first: Maria

middle: E

last: Figueroa

last: Passegué


title: Transcriptomic analysis of monocyte to macrophage differentiation in the colon

city: Edinburgh

first: Anika

last: Schridde

address: 47 Little France Crescent

country: United Kingdom

institute: University of Edinburgh

summary: Intestinal macrophages rely on the constant replenishment by bone marrow derived Ly6Chigh monocytes in the adult organism. The developmental path from monocytes towards intestinal macrophages locally in the tissue is defined by the loss of Ly6C and acquisition of MHCII and CX3CR1 expression. We used microarray analysis to further characterise this local differentiation process.

overall_design: We FACS purified the distinct stages defining monocyte to macrophage differentiation (P1-P4), identified by their differential expression of Ly6C, MHCII and CX3CR1, from colonic cell isolates from CX3CR1GFP/+ mice. The analysis was done using GeneChip® Mouse Gene 1.0 ST arrays from Affymetrix. Each population was analysed in triplicates. CX3CR1GFP/+ mice were used between 6-12 weeks of age.

first: Calum

middle: C

last: Bain

first: Marc

last: Dalod

first: Sandrine

last: Henri

first: Bernard

last: Malissen

first: Oliver

last: Pabst

first: Allan

last: Mowat


title: Gene expression profiles of human immature dendritic cells after 12h of co-cultivation with Aspergillus fumigatus, Candida albicans and LPS

city: Würzburg

first: Kristin

last: Czakai

address: Josef-Schneider-Straße 2

department: Department of Internal Medicine II

country: Germany

institute: University Hospital of Würzburg

summary: In a whole-transcriptome study, cellular responses of DCs confronted with the fungi A. fumigatus, C. albicans or the bacterial cell wall component lipopolysaccharide (LPS) were investigated. Therefore, DCs of four independent donors were harvested after 12 hours co-culture with A. fumigatus, C. albicans and LPS and analyzed with Affymetrix whole genome expression arrays. In general, transcriptomic analysis revealed a clustering of the A. fumigatus- and C. albicans-stimulated DCs. However, LPS and fungi-dependent gene expression showed more common similarities compared to the untreated control.

overall_design: Human DCs were generated from 4 independent, healthy blood donors. Monocyte-derived dendritic cells (moDCs) were either left untreated or co-cultivated with Aspergillus fumigatus 46645 germ tubes, Candida albicans SC5314 (MOI1) t or LPS (1µg/ml) for 12h.

first: Andreas

last: Dix


title: Expression data from GLUT4 overexpression in FaDu head and neck cancer cell line

status: Public on Mar 01 2017

city: Taipei

first: Michael

last: Hsiao

address: Academia Road, Section 2, Nankang, Taipei, 115, Ta

department: Genomics Research Center

country: Taiwan

institute: Academia Sinica

summary:
We demonstrate that GLUT4 up-regulation significantly increased cell migration and invasion in lower magligance head and neck cancer cell lines in vitro.
We used microarrays to analyze the GLUT4 regulated gene expression underlying invasion-metastasis cascade.

overall_design: FaDu head and neck squamous cancer cells with GLUT4 overexpression were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Yu-Chan

last: Chang


title: Immunologic Effects of a Peptide Vaccine with Intralesional IFNgamma For Treatment of Melanoma

city: Doha

first: Francesco

middle: Maria

last: Marincola

address: Al Nasr Tower, AL Corniche Street, PO Box 26999

country: Qatar

institute: Sidra Medical and Research Center

summary: Introduction: Optimal approaches to induce T-cell infiltration of tumors are not known. Chemokines CXCL9, CXCL10, and CXCL11 support effector T-cell recruitment, and may be induced by IFNgamma. This study tests the hypothesis that intratumoral administration of IFNgamma will induce CXCL9-11, and will induce T-cell recruitment and anti-tumor immune signatures in melanoma metastases. Patients and Methods: Nine eligible patients were immunized with a vaccine comprised of 12 class I MHC-restricted melanoma peptides (12MP) and received IFNgamma intratumorally. Effects on the tumor microenvironment (TME) were evaluated in sequential tumor biopsies. Adverse events (AE; CTCAE v4) were recorded. T-cell responses to vaccination were assessed in peripheral blood (PBMC) by IFNgamma ELIspot assay. Tumor biopsies were evaluated for immune cell infiltration, chemokine protein expression and gene expression. Results: Vaccination and intratumoral administration of IFNgamma were well tolerated. Circulating T-cell responses to vaccine were detected in 6 of 9 patients. IFNgamma increased production of chemokines CXCL10, CXCL11, and CCL5 in patient tumors. Neither vaccination alone nor the addition of IFNgamma promoted immune cell infiltration or induced anti-tumor immune gene signatures. Conclusion: The cancer vaccine did not significantly increase T-cell infiltration of tumors. This study provides intriguing findings highlighting some of the limitations of intratumoral IFNgamma treatment. Although IFNgamma is pivotal in anti-tumor immunity, single intratumoral injection may induce secondary immune regulation that paradoxically limits immune infiltration and effector functions. Therefore, alternate dosing strategies or additional combinatorial treatments may be needed to optimally promote trafficking and retention of T-cells in tumor, which merit further study.

overall_design: Biopsies (incisional, core or excisional biopsies) of cutaneous or subcutaneous metastatic melanoma were obtained on day 1 (baseline, pre-treatment) (n=7), day 22 (1 week after the third vaccine) (n=7) and day 24 (48 hrs after intratumoral injection of IFNgamma (n=7). When possible, biopsies at day 24 included both a tumor injected with IFNgamma (n=7) and one uninjected (n=3).


title: Differentiation of human and murine induced pluripotent stem cells to microglia-like cells

status: Public on Mar 02 2017

city: Bethesda

first: Kory

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

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: Systems analysis of protective immune responses to RTS,S malaria vaccination in humans

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

institute: Stanford University

summary: We applied a systems biology approach to study immune responses in subjects receiving 3 consecutive immunizations with RTS,S/AS01 (RRR), or in those receiving 2 immunizations of RTS,S/AS01, following a primary immunization with adenoviral Ad35 (ARR) vector expressing circumsporozoite protein.

overall_design:
The clinical trial (NCT01366534) was conducted at Walter Reed Army Institute of Research (WRAIR) Malaria Vaccine Branch. 46 healthy malaria-naïve volunteers, randomized to two study arms participated in this study testing the efficacy of RTS,S and AdVac® malaria vaccine candidates. Study arm 1 (hereafter referred to as ARR), comprised of 25 volunteers who received the AdVac® vaccine composed of Ad35 vector expressing full length CSP, as a primary immunization, followed by two doses of RTS,S/AS01 vaccine. The subjects in the second arm, consisting of 21 volunteers, received three doses of RTS,S/AS01 (RRR regimen). Participants in both study arms were vaccinated at 28-day intervals, and subjected to controlled malaria infection 21 days following the final immunization. Controlled human malaria infection  (CHMI) challenge was administered through five bites from malaria-infected mosquitoes to mimic natural infection. Parasitemia was monitored for 28 days, and immunomonitoring continued for 159 days following challenge. The study also included 12 non-vaccinated subjects as infectivity controls.
Please note that the non-vaccinated subjects were not profiled by microarray; this cohort served only as infectivity controls, to confirm that the infection protocol was effective.

last: Kazmn

first: Bali

last: Pulendran


title: Expression data from  vehicle tumor associated macrophages (TAM) VS PLX3397 treated-TAM.

first: Jian-Yang

last: Ao

summary:
To test the difference genes expression of TAMs obtained from orthotopically implanted hepa1-6 tumors in C57BL/6 mice.Isolated TAMs were obtained from orthotopically implanted hepa1-6 tumors in C57BL/6 mice. Specimens were minced with scissors and digested by incubation for 1 h at 37°C in high-glucose DMEM (Life Technologies, CA) containing 0.1% collagenase IV (Sigma). After being washed in medium plus 10% FBS, the cell suspension was forced through a graded series of meshes to obtain single-cell suspensions and centrifuged at 400 g for 30–40 minutes at 18–20°C on layers of Lympholyte-M (Cedarlane Labs, Burlington, Ontario, Canada), after which the upper layer was removed, thus leaving the lymphocyte layer undisturbed at the interface. TAMs were sorted using Fluorescence-activated cell sorting (FACS, Becton Dickinson, Franklin Lakes, NJ) with CD45+, CD11b+, and F4/80+ (Becton Dickinson) according to the protocol listed at http://www.immgen.org/Protocols/ImmGen%20Cell%20prep%20and%20sorting%20SOP.pdf . TAMs growing in DMEM supplemented with 10% FBS were tested to determine their biological characteristics.
We used microarrays to detail the global programme of gene expression and identified vehicle-TAM and treated-TAM during this process.

overall_design: To test the difference genes expression of vehicle-TAM and PLX3397 treated-TAM.TAMs from mouse tumors were processed in Trizol within 4 h after sorting and then analyzed using whole-mouse genome Affymetrix Mouse Gene 1.0 ST Arrays.

first: Hui-Chuan

last: Sun


title: Ph-like acute lymphoblastic leukemia in adults is characterized by IgH-CRFL2 and JAK2 mutations and poor prognosis [HG-U133_Plus_2]

city: Munich

first: Tobias

last: Herold

address: Marchioninistr. 15

department: Department of Internal Medicine III

institute: University Hospital Grosshadern, Ludwig-Maximilians-University (LMU)

summary: Philadelphia-like B-cell precursor acute lymphoblastic leukemia (Ph-like ALL) is characterized by distinct genetic alterations and inferior prognosis in children and younger adults. The purpose of this study was the genetic and clinical characterization of Ph-like ALL in adults. Among 207 adult B-cell precursor ALL patients, 26 (13%) were classified as Ph-like using Affymetrix microarrays. The incidence of this subtype was 25% among 105 B-cell precursor ALL patients negative for BCR-ABL1 and MLL-translocations (B-other). All patients with IgH-CRLF2 translocation (38% vs 0%; p=0.002) or mutations in JAK2 (44% vs. 0%; p<0.001) were exclusively found in the Ph-like subgroup. Clinical and outcome analyses were restricted to patients treated within GMALL trials 06/99 and 07/03 (n=107). The complete remission (CR) rate after induction was 100% for Ph-like (n=19) and B-other patients (n=40). After induction, significantly fewer Ph-like patients reached molecular CR (33% vs 79%; p=0.01). At 5 years, the Ph-like ALL subgroup had a lower probability of continuous CR (24% vs 62%; p<0.001) and overall survival (22% vs 64%; p=0.006) compared to B-other ALL patients. Subsequent analysis led to a clinically applicable algorithm identifying this patient subset with a specificity of 100%. Our study is the first to demonstrate that the profile of genetic events in adult Ph-like ALL resembles pediatric Ph-like ALL and differs from B-other ALL. The Ph-like phenotype associates with inferior outcomes in intensively treated adult ALL patients. Ph-like adult ALL should be recognized as a distinct, high-risk entity and further research on improved diagnostic and therapeutic approaches is needed.

overall_design: Analysis of 207 samples of bone marrow mononuclear cells (98 Affymetrix HG-U133 2.0 Plus Chip; 109 Affymetrix HG-U133 A&B Set) from adult patients with acute lymphoblastic leukemia (ALL).

first: Martin

last: Neumann

first: Stephanie

last: Schneider

first: Klaus

middle: H

last: Metzeler

first: Vindi

last: Jurinovic

first: Nikola

middle: P

last: Konstandin

first: Stefan

last: Bohlander

first: Ulrich

last: Mansmann

first: Wolfgang

last: Hiddemann

last: Dreyling

first: Claudia

middle: D

last: Baldus

first: Karsten

last: Spiekermann


title: Expression data


title: Expression data from M(LPS+IFNγ) and M(IL4)

summary:
Human monocyte THP-1 cells obtained from ATCC were cultured in RPMI 1640 (Invitrogen, Carlsbad, CA) containing 10% FBS and supplemented with 10 mM Hepes (Gibco BRL). THP-1 was differentiated into macrophages by 24-h incubation with 160 nM phorbol 12-myristate 13-acetate (PMA; Sigma, St. Louis, MO) followed by 24-h incubation in RPMI medium. Macrophages were further polarized to M1 macrophages by incubation with 10 pg/ml of lipopolysaccharide (LPS; Sigma) and 20 ng/ml of interferon (IFN)-γ (R&D Systems, MN) and are referred to as M(LPS+IFN-γ) cells. M2 macrophages were obtained by incubation with 20 ng/ml of interleukin (IL)-4 (R&D Systems) and are referred to as M(IL4) cells. To test the represented polarization marker of PMA differentiated-THP-1 macrophages stimulated with 20 ng ml(-1) IFNγ + 10 pg ml(-1) LPS and 20 ng ml(-1) IL-4, which are known to influence macrophage polarization in vetro into the M1 and M2 state, respectively.
We used microarrays to detail the gene expression pools to identify distinct M1 and M2 state during this process.

overall_design: To test the polarization of macrophage. PMA differentiated-THP-1 macrophages were stimulated with IFNγ+LPS and IL-4. THP-1 derived macrophages, including M(LPS+INFγ) and M(IL4) cells, were processed in Trizol and then analyzed using the Affymetrix U133 Array platform.


title: Xenografts of human pluripotent stem cells and embryonal carcinoma cells

status: Public on Feb 24 2017

city: Leiden

first: M.

middle: J.

last: Bouma

address: Einthovenweg 20

department: Anatomy & Embryology

country: Netherlands

institute: LUMC

summary:
Here we perfomed the Teratoma assay for a normal human embryonic stem cell line (H9(+Dox)), a human embryonic stem cell line with a mesendodermal differentiation bias (H9Hyb), a normal human induced pluripotent stem cell line (LU07), a human induced pluripotent stem cell line with reactivated transgenes (LU07+Dox) and a human embryonal carcinoma cell line (EC) and anayzed their gene expression.
The ability to form teratomas in vivo containing multiple somatic cell types is regarded as functional evidence of pluripotency for human pluripotent stem cells (hPSCs). Since the Teratoma assay is animal-dependent, laborious and only qualitative, the PluriTest and the hPSC ScoreCard assay have been developed as in vitro alternatives. Here we compared normal hPSCs, induced hPSCs (hiPSCs) with reactivated reprogramming transgenes and human embryonal carcinoma (hEC) cells in these assays. While normal hPSCs gave rise to typical teratomas, the xenografts of the hEC cells and the hiPSCs with reactivated reprogramming transgenes were largely undifferentiated and malignant. The hPSC ScoreCard assay confirmed the line-specific differentiation propensities in vitro. However, when undifferentiated cells were analysed with PluriTest only hEC cells were identified as abnormal whereas all other cell lines were indistinguishable and resembled normal hPSCs. Our results indicate that pluripotency assays are best selected on the basis of intended downstream applications.

overall_design: Total RNA from 1-3 xenografts were analyzed

first: Marga

middle: J


title: Differential microRNA gene expression between normal and aberrant late lung development induced by hyperoxia in mice

status: Public on Feb 25 2017

city: Bad Nauheim

first: Rory

last: Morty

address: Parkstr. 1

department: W.G. Kerckhoff-Institut

institute: MPI für Herz- und Lungenforschung

summary: Newborn mouse pups were exposed either to normoxia (21% O2) or to hyperoxia (85% O2) since the day of birth. Lungs were harvested at P2.5, P3.5, P5.5 and P14.5 and homogenized for a downstream microRNA (miR) microarray in order to compare the differential expression of miRs between normoxia and hyperoxia group. Several miRs appeared to be dysregulated, mainly and with a higher significance, at P5.5 and P14.5.

overall_design: Pups were randomized on the day of birth and litters were balanced. 4 cages were placed in normoxia whereas 4 cages in hyperoxia. Then, pups of the same age being placed in normoxia or hyperoxia were sacrificed on the same time-point. Total number of samples: 32.


title: Expression data from breast cancer bone metastasis

status: Public on Feb 23 2017

city: Basel

first: Tim

last: Roloff

address: Maulbeerstrasse 66

department: Functional Genomics

country: Switzerland

institute: FMI


title: miR-34a negatively regulates alveolarization in a BPD animal model

summary: Newborn mice were concomitantly treated with antagomiR-scrambled (SCR) or antagomiR-34a (A34a) and exposed either to normoxia (21% O2) or hyperoxia (85% O2). Lungs were harvested at two different time-points, P5.5 and P14.5, in order to compare the differential mRNA expression between the 4 groups. Unfortunately, few changes in mRNA expression were detected.

overall_design: Mouse pups were randomized and litter size was balanced on the same day of birth. For each time-point, 4 groups were designed: normoxia-SCR, normoxia-A34a, hyperoxia-SCR and hyperoxia-A34a. Comparisons were performed between the 4 groups of the same time-point for each time-point. Total number of samples: 32.


title: The expression profile of Cetuximab resistance in head-and-neck squamous cell carcinoma cells.

first: Wei-Lun

last: Hwang

address: No.155, Sec.2, Linong Street

department: Department of Biotechnology and Laboratory Science in Medicine

institute: National Yang Ming Chiao Tung University

summary:
Cetuximab (Erbitux) is an antibody drug against EGFR and commonly used in late stage HNSCC and metastatic colorectal cancer. The oncogenic mutation of certain genes are known to drive Cetuximab resistance such as K-RAS or b-RAF mutation. The aberrant activation of signaling pathways in the presence of Cetuximab treatment to overcome cellular stress contribute to acquired resistance to Cetuximab as well. To better understand the mechanisms and molecular patterns of Cetuximab resistant cells, the Cetuximab resistant cells are trained for examining the gene expression profile.
The gene expression array is used for identify the molecular signature governing the Cetuximab resitance.

overall_design: The OECM-1 cells were cultured in the presence of 300ug/ml to 1000ug/ml of Cetuximab (Erbitux) for more than 30 passages to establish the Cetuximab-resnstant clone, OER (OECM1-Erbitux resistance cells).  The cetuximab resistant genes are assessed by comparing the OER cells to its parental cells, OECM-1.

first: Muh-Hwa

last: Yang


title: Contribution of BET proteins to androgen (DHT)-stimulated gene expression program

status: Public on Feb 21 2017

city: North Chicago

first: Xin

last: Lu

state: IL

address: 1 North Waukegan Rd

department: Oncology Discovery

institute: Abbvie

summary: Competitive inhibitors of acetyl-lysine binding to the bromodomains of the BET (bromodomain and extra terminal) family are being developed for the treatment of solid and heme malignancies.  BET family member BRD4 function at enhancers/super-enhancers has been shown to sustain signal-dependent or pathogenic gene expression programs. Here we tested the hypothesis that the transcription factor drivers of castration-resistant prostate cancer (CRPC) clinical progression, including the Androgen Receptor (AR), are critically dependent on BRD4 and thus represent a sensitive solid tumor indication for the BET inhibitor ABBV-075.  DHT-stimulated transcription of AR target genes was inhibited by ABBV-075 without significant effect on AR protein expression.  Further, ABBV-075 disrupted DHT-stimulated recruitment of BET family member BRD4 to gene regulatory regions co-occupied by AR, including the well-established PSA and TMPRSS2 enhancers.  Persistent BET inhibition disrupted the composition and function of AR occupied enhancers as measured by a reduction in AR and H3K27Ac ChIP signal and inhibition of eRNA transcription.  ABBV-075 displayed potent anti-proliferative activity in multiple models of resistance to second generation anti-androgens and inhibited the activity of AR-V7 and the AR LBD gain-of-function mutations, F877L and L702H.  ABBV-075 was also a potent inhibitor of MYC and the TMPRSS2-ETS fusion protein, important parallel transcription factor drivers of CRPC.

overall_design: A total of 8 samples were included in this representative study that includes replicates of the EtOH and DHT treated samples.  Enzalutamide treatment is included as a reference compound for the DHT-activated AR pathway, and three doses of the BET inhibitor ABBV-075

first: Emily

last: Faivre

first: Paul

last: Hessler

first: Tamar

last: Uziel


title: MLL is essential for NUP98-HOXA9-induced leukemia

city: Chuo-ku

first: Yutaka

last: Shima

state: Tokyo

address: 5-1-1 Tsukiji

department: Division of Hematological Malignancy

country: Japan

institute: National Cancer Center

summary: Rearrangements involving the NUP98 gene resulting in fusions to several partner genes occur in acute myeloid leukemia and myelodysplastic syndromes. This study demonstrates that the second FG repeat domain of the NUP98 moiety of the NUP98-HOXA9 fusion protein is important for its cell immortalization and leukemogenesis activities. We demonstrate that NUP98-HOXA9 interacts with MLL via this FG repeat domain and that, in the absence of MLL, NUP98-HOXA9-induced cell immortalization and leukemogenesis are severely inhibited. Molecular analyses indicate that MLL is important for the recruitment of NUP98-HOXA9 to the HOXA locus and for NUP98-HOXA9-induced HOXA gene expression. Our data indicate that MLL is crucial for NUP98-HOXA9 leukemia initiation.

overall_design: To identify the regulated genes by the NUP98 moiety of NUP98-HOXA9, we performed gene expression profiling in full-length NUP98-HOXA9- and NUP98-HOXA9 deletion mutant-expressing cells.

first: Issay

last: Kitabayashi


title: DNA methylation profiles of human umbilical vein endothelial cells (HUVECs)

status: Public on Feb 20 2017

city: Aachen

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

institute: RWTH Aachen University

type: Methylation profiling by genome tiling array

summary: Replicative senescence has major impact on function and integrity of cell preparations. DNA-methylation (DNAm) changes are continuously acquired at specific CpG dinucleotides during in vitro culture. Such modifications can be used to estimate the state of cellular senescence for quality control of cell preparations. It is however unclear how senescence-associated DNAm changes are regulated and if they occur simultaneously throughout cell populations. In this study, we analyzed global DNAm profiles of human mesenchymal stem cells (MSCs) and human umbilical vein endothelial cells (HUVEC) to demonstrate that senescence-associated DNAm changes are overall similar in these different cell types. Subsequently, an Epigenetic-Senescence-Signature, based on six CpGs, was either analyzed by pyrosequencing or by barcoded bisulfite amplicon sequencing. There was a good correlation between predicted and real passage numbers in bulk populations of MSCs (R² = 0.67) and HUVECs (R² = 0.97).

overall_design: Bisulphite converted DNA of early (P4) and late passages (P20,P18,P13) from 3 donors was hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Julia

last: Franzen

first: Anne

last: Zirkel

first: Jonathon

last: Blake

first: Björn

last: Rath

first: Vladimir

last: Benes

first: Argyris

last: Papantonis


title: Unique DNA methylation signature in HPV-positive head and neck squamous cell carcinomas

status: Public on Feb 18 2017

city: Lyon

first: Zdenko

last: Herceg

address: 25 avenue Tony Garnier CS 90627

department: EGM

country: France

institute: IARC

summary:
Background. Head and neck squamous cell carcinomas (HNSCCs) represent a heterogeneous group of cancers, for which human papilloma virus (HPV) infection is an emerging risk factor. Previous studies showed promoter hypermethylation in HPV(+) oropharyngeal cancers, but only few consistent target genes have been so far described and the evidence of a functional impact on gene expression is still limited.
Methods. We performed global and stratified pooled analyses of epigenome-wide data in HNSCCs based on the Illumina HumanMethylation450 bead-array data in order to identify tissue-specific components and common viral epigenetic targets in HPV-associated tumours .
Results. We identified novel differentially methylated CpGs and regions associated with viral infection that are independent of the anatomic site. In particular, most hypomethylated regions were characterized by a marked loss of CpG island boundaries, which showed significant correlations with expression of neighbouring genes. Moreover, a subset of only 5 CpGs in few hypomethylated regions predicted HPV status with a high level of specificity in different cohorts. Finally, this signature was a better predictor of survival compared with HPV status determined by viral gene expression by RNA-Sequencing in the TCGA cohort.
Conclusions. We identified a novel epigenetic signature of HPV infection in HNSCCs which is independent of the anatomic site, is functionally correlated with gene expression and may be leveraged for improved stratification of prognosis in HNSCCs.

overall_design: In total 12 samples from French head and neck cancer patients were processed. Data for 11 samples are provided as one sample did not pass the quality checks.

first: Davide

last: Degli Esposti

first: Athena

last: Sklias

first: Vincent

last: Cahais

first: Ellen

last: Van Obberghen-Schilling


title: Ph-like acute lymphoblastic leukemia in adults is characterized by IgH-CRFL2 and JAK2 mutations and poor prognosis

first: Tobias

last: Herold


title: Expression data of undifferentiated cells and xenografts of human pluripotent stem cells and embryonal carcinoma cells

first: M.

last: Bouma


title: Expression data from breast cancer bone metastasis [EO771]

first: Tim

last: Roloff

summary:
The goal of this study was to evaluate genes that are differentially expressed in the bone stroma when breast cancer metastasis are present. We focused our attention on bone stroma cells to understand how the dissemination and growth of tumor cells can impact on the bone environment. Moreover, we aimed to identify potential targets to inhibit the cross talk between cancer cells and tumor microenvironment in bone metastasis.
EO771 breast cancer cell line were engineered to express luciferase and GFP, and injected in C57BL/6 mice by the intracardiac route to obtain bone metastasis. Tumor growth was monitored in-vivo by bioluminescence for 2 weeks. Endothelial cells and osteoblasts were isolated from the long bones of tumor-bearing and tumor-free mice to identify genes differentially expressed.

overall_design: Bone marrow single cell suspensions from tumor-free or tumor-bearing mice (n=6-10 samples) were prepared by grinding bones in a mortar followed by enzymatic digestion of the bone powder for 1 hour at 37°C with 1 mg/ml collagenase, 1 mg/ml dispase and 50KU/ml DNAse. Stroma cells and hematopoietic fractions were enriched by discontinuous percoll density gradient separation (1.065 g/L and 1.115 g/L).  Remaining red blood cells were lysed and the single cell population was stained to isolate two different stroma cells by FACS: osteoblasts (OBctr) (OBtum), were identified as GFP-TR119-CD45-SCA1-CD31-CD51+, and endothelial cells (ECctr) (ECtum) were identified as GFP-TR119-CD45-SCA1+CD31+.

first: Jason

middle: W

last: Gill

first: Alessia

last: Bottos

first: Nancy

last: Hynes

first: Aleksandra

last: Filipowicz-Wodnar

first: Thiry

last: Stéphane


title: Expression data from ectopic RUNX2 over-expression in Ca9-22 cells

status: Public on Feb 13 2017

first: Wei-Min

last: Chang

state: Not Applicable

address: 128 Academia Road, Section 2, Nankang,

summary: To examine the transcription targets of RUNX2 in OSCC cells, we preformed the Affymetrix Human Genome U133 Plus 2.0 Array with ectopic RUNX2 or empty vectors in Ca9-22 cells.

overall_design: Total RNA was collected from empty vector or RUNX2 expression Ca9-22 cells.

first: Michael

last: Hsiao

first: Shine-Gwo

last: Shiah


title: Gene expression profiling of supporting, interstitial/stromal, and germ cells during the formation of the testis cords

city: Krakow

first: Dagmara

last: Podkowa

address: Gronostajowa 7

country: Poland

institute: Jagiellonian University

summary: The aim of this study was to analyze the gene expression profile for three main cell lines (supporting, interstitial/stromal, and germ cells) isolated from developing gonads during the process of the testis cord and ovarian cyst formation (between TS13 and TS34).

overall_design: Three cell lines (supporting, interstitial/stromal, and germ cells) were isolated from murine fetal XX and XY gonads at three time points (TS13, TS24, and TS34). Transgenic mouse strains with the expression of cell type specific fluorescent markers were used to isolate the cell lines. Cells were sorted using FACS method and then the RNA was extracted.

first: D


title: Expression data from breast cancer bone metastasis [MDA-MB 231 scp1833]

summary:
The goal of this study was to evaluate genes that are differentially expressed in the bone stroma when breast cancer metastasis are present. We focused our attention on bone stroma cells to understand how the dissemination and growth of tumor cells can impact on the bone environment. Moreover, we aimed to identify potential targets to inhibit the cross talk between cancer cells and tumor microenvironment in bone metastasis.
MDA-MB 231 scp1833 breast cancer cell line were engineered to express luciferase and GFP, and injected in NOD-SCID mice by the intracardiac route to obtain bone metastasis. Tumor growth was monitored in-vivo by bioluminescence for 2 weeks. Endothelial cells and osteoblasts were isolated from the long bones of tumor-bearing and tumor-free mice to identify genes differentially expressed.


title: Expression data of human hypopharyngeal tumor cells (FaDu)

first: Kai-Chun

last: Li

address: No. 1, Sec. 4, Roosevelt Road

institute: National Taiwan University

summary:
FaDu cells were infected with lentivirus containing sh-luciferase plasmid to compared with cells infected with sh-G9a containing lentivirus.
We performed microarray analysis to identify the genes possibly regulated by G9a in FaDu cells

overall_design: In our study, we found that G9a positively directs the growth adventage of HNSCC cells. Inhibition of G9a induced autophagic cell death. To further indentify the downstream  mechanism, we perform affymetrix microarray to identify the downstream target of G9a in negatively regulation of autophagy.

first: Kuo-Tai

last: Hua

first: Yi-Shen

last: Lin


title: Expression data from active rheumatoid arthritis patients and healthy control.

city: Beijing

first: Jianping

last: Guo

address: NO.11,Xizhimen South Street,Xicheng District

department: Rheumatology & Immunology

institute: Peking University, People's Hospital

summary:
Rheumatoid arthritis (RA) is a systemic autoimmune disease and its underlying molecular mechanisms are still poorly understood. Previously a CD4 T-cell microarray study has only focused arthritis patients. We aimed to compare the molecular profiles of active RA versus healthy control in CD4 T cells.
We used microarrays to detail the global programme of gene expression in active RA and healthy control.

overall_design: The highly purified peripheral blood CD4 T cells were isolated from 13 RA patients with active disease and from 9 healthy individuals for RNA extraction and hybridization on Affymetrix microarrays.

first: Hua

last: Ye

first: Jing

last: Zhang


title: Effect of Hypercapnia on Murine Ventilator-Induced Lung Injury

status: Public on Feb 22 2017

city: Toronto

first: Gail

last: Otulakowski

state: ON

address: 555 University Ave

department: Physiology & Experimental Medicine

country: Canada

institute: Hospital for Sick Children Research Institute

summary:
Addition of CO2 to the inspired gas can ameliorate lung injury during high tidal volume mechanical ventilation in animal models. Although some effects of hypercapnia on physiology and cell signaling have been characterized, we hypothesized that assessment of genome-wide gene expression patterns would reveal novel pathways of protection.
We subjected male C57BL/6J mice to non-injurious low stretch (tidal vol = 10 mL/kg, PEEP = 2 cm H2O) or injurious high stretch (tidal volume approx 35 mL/kg, PEEP = 0 cm H2O) mechanical ventilation for 3 hours under normocapnia (FiCO2 = 0) or hypercapnia (FiCO2 = 0.12).

overall_design: Lung RNA was extracted from mice randomized to the following groups: non-ventilated (n = 5); low stretch normocapnia (n = 5); low stretch hypercapnia (n = 5); high stretch normocapnia (n = 10); high stretch hypercapnia (n = 10).  Each RNA sample was analyzed on a separate microarray chip (no pooled samples).

first: Brian

last: Kavanagh


title: Ethnic specific genetic variation alters smoking associated DNA methylation at HIV co-receptor GPR15

city: Iowa City

first: Robert

last: Philibert

state: Iowa

address: MEB, 500 Newton Road, Room 2-126D

department: Psychiatry

institute: University of Iowa

summary: Genome wide DNA methylation profiling of smokers and non-smokers in PBMC samples. The Illumina Infinium 450k Human DNA methylation Beadchip v1.1  was used to obtain DNA methylation profiles across  485,577 CpGs in PBMC samples. Samples included 24 smokers and 28 non-smokers.

overall_design: Bisulfite converted DNA from the 52 samples were hybridized to the Illumina Infinium 450k Human Methylation Beadchip v1.1


title: Transcriptome analysis of a FACS-sorted human intersitial cells of Cajal (ICC) [array]

city: Rochester

first: Tamas

last: Ordog

state: MN

address: 200 1st St SW

institute: Mayo Clinic

summary:
Interstitial cells of Cajal (ICC) are electrical pacemakers and mediators of neuromuscular neurotransmission in the gastrointestinal tract. Gastrointestinal stromal tumors (GIST) arise within the ICC lineage due to activating KIT/PDGFRA mutations. In this study we developed a method for isolation of human ICC by immunolabeling and fluorescence-activated cell sorting (FACS). Briefly, human gastric musculature was dissociated and incubated with antibodies against CD45, FCER1A, CD11B, KIT, and CD34. ICC (defined as HP-KIT+CD34- cells), NOT ICC (defined as HP-KIT-CD34- cells), and hematopoietic (HP) cells (defined as HP+ cells) were isolated using FACS. Microarray was performed on ICC, NOT ICC, HP+ cells, and unfractionated gastric tunica muscularis.  This study utilized micorarray for the phenotypic characterization of FACS-sorted human ICC, allowing comparison of ICC to other cells of the gastric musculature, including GIST.
De-identified human gastric tissues obtained as surgical excess tissue from patients undergoing bariatric operations. This study utilized oligonucleotide microarray analysis to characterize the transcriptome of FACS-sorted human ICC.

overall_design: Total RNA from ICC, NOT ICC, HP+ cells, and unfractionated gastric tunica muscularis was isolated.  Oligonucleotide microarray studies were performed using Affymetrix GeneChip Human Genome U133 Plus 2.0 array.


title: Genome-wide methylation approach identifies a novel hypermethylated gene panel in ulcerative colitis

status: Public on Feb 11 2017

city: Cheonan

first: Keunsoo

last: Kang

address: 119 Dandae-ro

country: South Korea

institute: Dankook University

summary: Genome wide DNA methylation profiling of three normal (N) and eight ulcerative colitis (UC) samples as well as one human colon cancer cell (HCT116) . The Illumina Infinium 450k Human DNA methylation platform was used to obtain DNA methylation profiles across approximately 480,000 CpGs.

overall_design: Bisulphite converted DNA from the 12 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip.

first: K

first: J

last: Bae

last: Han

first: E

middle: S

last: Kim

first: T

last: Yi


title: Angptl4 is upregulated under inflammatory conditions in the bone marrow of mice, expands myeloid progenitors, and accelerates reconstitution of platelets after myelosuppressive therapy

first: Bernd

last: Denecke

state: NRW

address: Pauwelsstrasse 30

department: IZKF Aachen

summary: Upon inflammation, myeloid cell generation in the bone marrow (BM) is broadly enhanced by the action of induced cytokines, which are produced locally or at multiple sites throughout the body. Using microarray studies, we show that Angptl4 is a predominantly upregulated cytokine in the BM during systemic inflammatory conditions. Functionally we found  recombinant murine Angptl4 (rmAngptl4) to stimulate the proliferation of myeloid CFUs in vitro. Upon repeated in vivo injections, rmAngptl4 increased BM progenitor cell frequency, and this was paralleled by a relative increase in phenotypically defined granulocyte-macrophage progenitors (GMPs). Furthermore, in vivo treatment with rmAngptl4 resulted in elevated platelet counts in steady-state mice and a significantly accelerated reconstitution of platelets in post-transplanted mice after myelosuppressive therapy. In contrast, transplantation of BM cells from donor mice pre-treated with rmAngptl4 had no effect on the recovery of platelets. The administration of rmAngptl4 additionally increased the number of CD61+CD41low-expressing megakaryocytes (MKs) in the BM of steady-state and in the spleen of transplanted mice as well as after in vitro MK-differentiation from hematopoietic stem and progenitor cells. Furthermore, using a stat3 reporter knockin model, we show that rmAngptl4 induces de novo stat3 expression in immature MKs which could be important for the effective expansion of MKs after myelosuppressive therapy. In summary our data suggest that Angptl4 plays a complementary role in hematopoiesis during emergency situations like sepsis. The use of Angptl4 in the setting of autologous stem cell transplantation could represent a potential approach for accelerating the reconstitution of megakaryopoiesis.

overall_design: in total 4 probes: 2 replica of BM cells isolated from PBS- and LPS-treated C57BL/6N mice

first: Patrick

last: Ziegler

first: Anne

last: Schumacher

first: Jasmin

last: Stahlschmidt

first: Susanne

first: Tim

last: Brümmendorf


title: Healthy adults' blood gene expression who ingested Salacia reticulata plant extract

city: Minato-ku

first: Yuriko

last: Oda

address: 7-3, Akasaka 9-Chome

institute: Fujifilm Corporation

summary: In human volunteers, we evaluated changes in gene expression profiles, immunological indices, and  intestinal microbiota of blood cells in subjects consuming a S.reticulata extract. Thirty healthy Japanese males were split randomly into a group ingesting 240 mg/day of S.reticulata extract -containing tablets for 4 weeks and a control group ingesting placebo tablets.   Ingestion of the S.reticulata extract improved T cell proliferation and other immunological indices, and changed intestinal microbiota, increasing Bifidobacterium and Lactobacillales and decreasing Clostridium bacteria. Expression levels of many immuno-relevant genes were altered.  We have shown the S.reticulata extract to enhance human immune functions.

overall_design: In the S.reticulata extract ingestion group, 7 subjects (14 samples) were chosen randomly and subjected to pre- (B) and post-ingestion(T) gene expression analysis.

first: Fumitaka

last: Ueda

first: Masanori

last: Utsuyama

first: Asuka

last: Kamei

first: Chihaya

last: Kakinuma

first: Keiko

last: Abe

first: Katsuiku

last: Hirokawa


title: Expression data from epidermal and dorsal root ganglion tissues of wild-type and mutant mice with mechanosensory deficit

city: Milwaukee

first: Cheryl

last: Stucky

state: WI

address: 8701 Watertown Plank Road

institute: Medical College of Wisconsin

summary:
A novel mouse line was found to exhibit prominent mechanosensory deficits both behaviorally and at the primary sensory afferents, and exhibits decreased ATP release from the skin.
Microarray analysis was used to determine transcriptomic differences that may underlie the mechanosensory deficit in the mutant mouse, and to explore the decreased response of the mutant mouse to an inflammatory insult.

overall_design: Tissues were obtained from wild-type mice and from mutant mechanosensory-deficient mice (Keratin14Cre-TRPA1(fl/fl) mice).  For each genotype, there were 3 biological replicates of the following groups: naive control epidermis, CFA hindpaw-injected epidermis, and naïve dorsal root ganglia). mRNA was extracted from isolated epidermis or from dorsal root ganglia. mRNA was processed and hybridizated on Affymetrix microarrays.

first: Katherine

last: Zappia

first: Andy

last: Weyer

middle: L


title: Multicomponent Signatures for Predicting Epigenomic Treatment Efficacy

status: Public on Feb 16 2017

city: Boston

first: William Evan

last: Johnson

address: 72 E Concord Street

department: Computational Biomedicine

institute: Boston University

summary: Genome wide DNA methylation profiling of breast cancer cell lines and mouse xenograft, treated with HDAC Inhibitors.

overall_design: Bisulphite converted DNA from the 48 samples were hybridised to the Illumina Infinium 450K Human Methylation Beadchip

first: Andrea

last: Bild

first: Stefanie

last: Jeffrey


title: Mining the microbiome for modulatory effects on the murine intestinal transcriptome

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Within the human gut reside diverse microbes coexisting with the host in a mutually advantageous relationship. We comprehensively identified the modulatory effects of phylogenetically diverse human gut microbes on the murine intestinal transcriptome. Gene-expression profiles were generated from the whole-tissue intestinal RNA of mice colonized with various single microbial strains. The selection of microbe-specific effects, from the transcriptional response, yielded only a small number of transcripts, indicating that symbiotic microbes have only limited effects on the gut transcriptome overall. Moreover, none of these microbe-specific transcripts was uniformly induced by all microbes. Interestingly, these responsive transcripts were induced by some microbes but repressed by others, suggesting different microbes can have diametrically opposed consequences.

overall_design: At precisely 4 weeks of age, C57BL/6 germ free (GF) mice were colonized by oral gavage with one bacterial species isolated from the human microbiota. Mice were maintained under gnotobiotic conditions for 2 weeks, after which they were assessed by transcriptional profiling of the colon and the small intestine. Effects of over 30 individual microbes were studied on the intestinal transcriptome. GF controls were collected throughout the duration of this study.  To reduce variability, intestinal profiling included 4 batches and each batch of microbially colonized intestines was profiled together with at least two replicates of GF controls. The same segment of the distal colon (0.3cm long- 3cm away from rectum) and three segments (0.3cm each) from the same mid-section of duodenum, jejunum and ileum of the small intestine were collected from all mice and homogenized in Trizol. RNA from intestinal tissue was amplified, labeled and hybridized to Affymetrix Mouse Gene 1.0 ST Arrays.

first: Naama

last: Geva-Zatorsky

first: Esen

last: Sefik

first: Diane

last: Mathis

first: Christophe

last: Benoist

first: Dennis

last: Kasper


title: Image-guided genomics of phenotypically heterogeneous populations reveals vascular signaling during symbiotic collective cancer invasion

status: Public on Feb 10 2017

city: Atlanta

first: Adam

middle: I

last: Marcus

state: GA

address: 1365C Clifton Rd., N.E., Room 4092

institute: Emory University

summary:
To probe the phenotypic heterogeneity found in cell populations, we developed an image-guided genomics technique termed spatiotemporal genomic and cellular analysis (SaGA) that allows for precise selection and amplification of living and rare cells. SaGA was used on collectively invading 3-D cancer cell packs to create purified leader and follower cell lines. The leader cell cultures are phenotypically stable and highly invasive in contrast to follower cultures, which show phenotypic plasticity over time and minimally invade in a sheet-like pattern. Genomic and molecular interrogation reveals an atypical VEGF-based vasculogenesis signaling that facilitates recruitment of follower cells but not for leader cell motility itself, which instead utilizes focal adhesion kinase-fibronectin signaling. While leader cells provide an escape mechanism for followers, follower cells in turn provide leaders with increased growth and survival. These data support a symbiotic model of collective invasion where phenotypically distinct cell types cooperate to promote their escape.
A single tumor can harbor distinct genetic and epigenetic cellular sub-populations that drive tumor initiation and progression. This intratumor heterogeneity is proposed to be one of the major confounding factors of treatment causing relapse and poor clinical outcome1. Genomic instability and epigenetic modifications generate intratumor heterogeneity creating distinct genetic and epigenetic sub-populations or clones. A branched tumor evolutionary architecture can emerge containing the plasticity to progress under harsh environmental conditions and thwart therapeutic attempts to eradicate the tumor. It can be argued that until we discover how intratumor heterogeneity can be circumvented, precision oncology initiatives may fall short of expectations.
Single cell sequencing methodologies have improved the genomic, transcriptomic, and epigenomic resolution of clonal tumor populations; however, the phenotypic implications of these alterations remain unclear. This is partly due to experimental challenges and is compounded by phenotypic plasticity that allows cancer cells to adapt to local changes in the microenvironment, without changes to the genome itself (e.g., epithelial to mesenchymal transition). Despite repeated observations that a small number of rare cancer cells or clones, hidden within a larger tumor population can drive tumor growth and spread, studies linking single cell or clonal phenotypes with genomic data have been limited.
To probe the biology of a rare and phenotypically heterogeneous cell populations, single cells or subclones need to be isolated based upon user-defined criteria, instead of a random isolation approach; therefore, we developed a technique to image live cells within a biologically relevant 3-D environment, select a cell or cellular group based upon user-defined criteria, extract the cell(s), and subject the cell(s) to genomic and molecular analyses. In this way, we can purify, amplify, and systematically dissect the biologies of rare cells. This new technique, termed spatiotemporal genomic and cellular analysis (SaGA), was used to dissect the phenotypic heterogeneity of collective cancer cell invasion in a 3-D lung cancer model. These data incorporate the first SaGA-derived leader and follower cell lines to reveal that leader cells utilize atypical vasculogenesis signaling machinery by secreting VEGF to attract follower cells in invasive cell chains. In contrast, follower cells support leader cell growth by increasing their mitotic efficiency. This relationship argues for a cellular symbiosis within the collective invasion pack. Furthermore, these data provide proof of concept that SaGA is a powerful technology for dissecting phenotypic heterogeneity within cancer cell populations.

overall_design: We isolated pure leader (L) and follower (F) cells using the image-guided genomics technique described in the manuscript and tested significant expression differences between these subpopulations relative to controls. The impact of the photoconversion process on gene expression was controlled by comparing invasive cells that have been photoconverted (IR) to invasive cells that were not photoconverted (NG). Any gene that significantly changed between these two conditions were denoted as alterations due to the photoconversion process and were consequently excluded from analysis.

first: J

last: Konen

first: E

last: Summerbell

first: B

last: Dwivedi

first: K

last: Galior

first: Y

last: Hou

first: L

last: Rusnak

first: A

last: Chen

last: Saltz

first: W

last: Zhou

last: Boise

first: P

last: Vertino

last: Cooper

last: Salaita

last: Kowalski


title: IL-15 sustains IL-7R independent ILC2 and ILC3 development

city: St. Louis

first: Marco

last: Colonna

state: Missouri

address: 509 S Euclid Ave

department: Pathology and Immunology

institute: Washington University in St. Louis

summary:
ILC3 contain 3 well-defined subsets, CCR6+ ILC3, NKp46+ ILC3, and CCR6–NKp46– DN ILC3. These subsets had not previously been transcriptionally compared and the extent to which they had shared or unique transcriptional profiles remained unclear.
We used microarray to determine transcriptional differences between these 3 subsets and to find putative factors that support the survival of CCR6+ ILC3 during cytokine depletion.

overall_design: ILC3 subsets were sorted from small intestine lamina propria, for RNA extraction and hybridization on Affymetrix microarrays.

first: Michelle

last: Robinette


title: Genes differentially expressed in long-term hematopoietic stem cells with latexin deletion

status: Public on Feb 09 2017

city: Lexington

first: Ying

last: Liang

state: KY

address: Health Sciences Research Bldg. Rm. 340, 1095 V.A. Drive

department: Toxicology and Cancer Biology

institute: University of Kentucky

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

overall_design: Refer to individual Series


title: Robust Stratification of Breast Cancer Subtypes

status: Public on Feb 15 2017

city: Nashville

first: Thomas

middle: Paul

last: Stricker

state: TN

address: 1161 21st Ave South, CC3309A

department: Pathology, Microbiology and Immunology

institute: Vanderbilt University

type: Expression profiling by high throughput sequencing

summary: Breast cancer, the second leading cause of cancer death of women worldwide, is a heterogenous disease with multiple different subtypes. These subtypes carry important implications for prognosis and therapy. Interestingly, it is known that these different subtypes not only have different biological behaviors, but also have distinct gene expression profiles. However, it has not been rigorously explored whether particular transcriptional isoforms are also differentially expressed among breast cancer subtypes, or whether transcript isoforms from the same sets of genes can be used to differentiate subtypes.  To address these questions, we analyzed the patterns of transcript isoform expression using a small set of RNA-sequencing data for eleven Estrogen Receptor positive (ER+) subtype and fifteen triple negative (TN) subtype tumors. We identified specific sets of isoforms that distinguish these tumor subtypes with higher fidelity than standard mRNA expression profiles. We found that alternate promoter usage, alternative splicing, and alternate 3’UTR usage are differentially regulated in breast cancer subtypes. Profiling of isoform expression in a second, independent cohort of 68 tumors confirmed that expression of splice isoforms differentiates breast cancer subtypes. Furthermore, analysis of RNAseq data from 594 cases from the TCGA cohort confirmed the ability of isoform usage to distinguish breast cancer subtypes. Also using our expression data, we identified several RNA processing factors that were differentially expressed between tumor subtypes and/or regulated by Estrogen Receptor, including YBX1, YBX2, MAGOH, MAGOHB, and PCBP2. RNAi knock-down of these RNA processing factors in MCF7 cells altered isoform expression. These results indicate that global dysregulation of splicing in breast cancer occurs in a subtype-specific and reproducible manner and is driven by specific differentially expressed RNA processing factors.

overall_design: RNAseq libraries for 11 ER+ human breast cancers and 14 triple negative human breast cancers were built and sequenced. The RNAseq data is from patients, so we will be making the raw sequencing reads available not through SRA, but will be hosted at the Protected Data Cloud at Bionimbus (https://bionimbus-pdc.opensciencedatacloud.org/). To obtain access to the raw sequencing data, you must have have your eRA, Shibboleth, or Oauth identifier added to the authorization list of a project. To do so, please send an email to accounts@occ-data.org, which will respond with a Data Use Agreement. Once signed and returned, the raw sequencing data will be made available for download.

first: Kevin

last: White

first: Christopher

last: Brown


title: Gene expression data of primary Osteosarcomas

city: Amsterdam

first: Richard

last: Volckmann

state: Noord-Holland

address: van der Boechorststraat 6a

department: Laboratory of Experimental Oncology and Radiobiology

institute: msterdam UMC and University of Amsterdam

summary: Affymetrix gene expression data of 21 high-grade osteosarcomas located in the extremities.This gene expression profiling was performed in order to evaluate the expression of candidate prognostic and therapeutic targets in high-grade osteosarcoma.

overall_design: 21 tumor samples

first: Massimo

last: Serra


title: Aberrant methylation-mediated silencing of microRNAs contributes to HPV-induced anchorage independence [methylation-Illumina]

first: Saskia

last: Wilting

address: De Boelelaan 1117

institute: VU University Medical Center

summary: Cervical cancer and a subset of anogenital and head-and-neck carcinomas are caused by persistent infection with high-risk types of the human papillomavirus (hrHPV). Early stages of hrHPV-induced carcinogenesis can be faithfully mimicked in vitro. A major hallmark of hrHPV-transformed cells is their ability to grow anchorage independently, an oncogenic trait known to depend on inactivation of tumour suppressor genes. This study used an in vitro model of hrHPV-induced transformation to delineate in a longitudinal manner to what extent DNA methylation-mediated silencing of tumour suppressive microRNAs (miRNAs) contributed to hrHPV-induced anchorage independence.  Genome-wide miRNA expression profiles were yielded from anchorage dependent (n=11) and independent passages (n=19) of 4 hrHPV-immortalised keratinocyte cell lines with and without demethylating treatment (DAC). Unsupervised clustering analysis showed that overall miRNA expression patterns discriminated between anchorage dependent and independent cells. Ten miRNA genes potentially silenced by methylation were selected and validated by bisulfite sequencing and methylation-specific PCR. Hsa-mir-129-2, -137, -935, -3663, -3665, and -4281 showed increased methylation in both HPV-transformed keratinocytes and cervical cancer cell lines compared to primary keratinocytes. Mature miRNAs derived from hsa-mir-129-2, -137, -3663, and -3665 decreased anchorage independence in cervical cancer cell lines. Finally, significantly increased methylation of hsa-mir-129-2, -935, -3663, -3665, and -4281 was observed in cervical (pre)cancerous lesions, underlining the clinical relevance of our findings.    In conclusion, methylation-mediated silencing of tumour suppressive miRNAs contributes to the acquisition of anchorage independence, supporting the importance of miRNAs during early stages of carcinogenesis and underlining their potential as both disease markers and therapeutic targets.

overall_design: Anchorage independent passages of 4 independent HPV-transformed keratinocyte cell lines (FK16A and FK16B containing HPV16 and FK18A and FK18B containing HPV18) were analysed by Infinium HumanMethylation450 BeadChip. In addition, primary human foreskin keratinocytes of 2 donors without HPV were included as normal controls.

middle: M

first: Viktorian

last: Miok

first: Annelieke

last: Jaspers

first: Debby

last: Boon

first: Hanne

last: Sørgård

first: Malin

last: Lando

first: Barbara

last: Snoek

first: Wessel

middle: N

last: van Wieringen

first: Chris

last: Meijer

first: Heidi

last: Lyng

first: Peter

last: Snijders

first: Renske

last: Steenbergen


title: Gene expression analysis of human macrophages exposed to lipoprotein lipase hydrolysis products

city: St. John's

first: Sherri

last: Christian

state: Newfoundland

address: 232 Elizabeth Ave

department: Biochemistry

institute: Memorial University of Newfoundland

summary:
Lipoprotein lipase (LPL) is an extracellular lipase that preferentially hydrolyses triglycerides in triglyceride-rich lipoproteins within the circulation. LPL expression in macrophages contributes to atherosclerosis. In addition, the hydrolysis products liberated from lipoprotein lipids by LPL causes lipid accumulation and impairs cholesterol efflux ability in macrophages. However, the effects of LPL hydrolysis products in modulating the transcript profiles within macrophages and their roles in foam cell formation are not completely understood.
We performed microarray analyses on THP-1 macrophages incubated with LPL hydrolysis products to identify differentially expressed genes.

overall_design: Human LPL was recombinantly expressed in HEK-293T cells. Heparinized media from cells expressing LPL or from control cells were used to hydrolyse total lipoproteins that were isolated from normolipidemic subjects. THP-1 macrophages were incubated with 0.68 mM (by unesterified fatty acid content) of LPL hydrolysis products, or non-hydrolysis products (of 0.03 mM by unesterified fatty acid content) for 18 hours (n=3). Total RNA was isolated from treated samples and it was used for human gene arrays.

first: Narmadaa

last: Thyagarajan

first: Robert


title: Genome-wide DNA methylation maps of histone deacetylase inhibition in triple-negative breast cancer

status: Public on Feb 14 2017

city: Santa Monica

first: Dave

last: Hoon

address: 2200 Santa Monica Boulevard

department: Translational Molecular Medicine

institute: Saint John's Cancer Institute

summary: Analysis of DNA methylation changes after prolonged exposure of triple-negative breast cancer cell lines to low doses of Panobinostat (LBH589), a pan-histone deacetylase inhibitor.

overall_design: Bisulfite-converted DNA was hybridized to the Illumina Infinium 450k Human Methylation BeadChip to generate genome-wide DNA methylation maps of  triple-negative cell lines cell types after histone deacetylase inhibition.

first: Diego

last: Marzese

first: Matthew

last: Salomon

first: Matias

last: Bustos


title: Gene expression profiling of plasmacytoid dendritic cells from cutaneous lymph nodes

city: MARSEILLE

first: Marc

last: DALOD

address: Parc Scientifique et Technologique de Luminy, 163 avenue de Luminy, Case 906, 13288 Marseille cedex 9

institute: CIML

summary: Plasmacytoid dendritic cells wre isolated from cutaneous lymph nodes of control C57BL/6 mice and used for microarray analysis.

overall_design: Plasmacytoid dendritic cells were isolated from cutaneous lymph nodes (CLNs) as previously described (Henri et al. 2010). Briefly, CLNs were cut into small pieces and digested for 20 min at room temperature with a mixture of type II collagenase (Worthington Biochemical) and DNase I (Sigma-Aldrich). The resulting cell suspension was treated with 5 mM EDTA to disrupt DC-T cell conjugates. After eliminating undigested material, light-density cells were enriched by centrifugation on an Optiprep solution (d = 1.32 g/mL, Abcys).

first: S

last: Henri

first: R

last: Chelbi

first: M

last: Dalod

first: B

last: Malissen


title: Impact of Cirrhosis on Endogenous Interferons During HCV Treatment with Direct Acting Antivirals

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

summary: Chronic hepatitis C virus (HCV) infection is now routinely treated with interferon (IFN)-free regimens composed of directly acting antiviral (DAA) agents.  Changes in hepatic and peripheral innate and adaptive immune function during DAA therapy associate with achieving a sustained virologic response (SVR). The present study explored the impact of cirrhosis on host endogenous interferon pathways during DAA therapy. mRNA and micro-RNA (miRNA) expression profiling was performed on paired pre- and end-of-treatment (EOT) liver biopsies from subjects treated with a 2 DAA regimen (sofosbuvir/ledipasvir [SOF/LDV]) for 12 weeks (n=4, 3 with cirrhosis) or a 3 DAA regimen (SOF/LDV with GS-9669 or GS-9451) for 6 weeks (n=6, 0 with cirrhosis). Nine of ten subjects achieved SVR, with one relapse in the GS-9669 treatment arm (ISHAK fibrosis 4). Hepatic interferon-stimulated gene expression was down-regulated in the liver of all subjects, with no observable impact of cirrhosis or duration of treatment. Hepatic down-regulation of all type-III IFNs was observed (IFNL1, IFNL2, IFNL3, IFNL4-ΔG), while IFNA2 expression, undetectable in all subjects pre-treatment, was detected in 3 of 9 subjects at EOT (all 3 achieved SVR).  Only the subject who relapsed had detectable IFNL4-ΔG expression in EOT liver.  No change in IFNB1, IFNG, or IFNA5 expression was observed, and expression of other type-I IFNs (IFNA1, IFNA4, IFNA5, IFNA6, IFNA8, IFNA16, IFNA17) was not detected pre- or post-treatment.  While expression of multiple miRNAs changed in liver tissue over the course of treatment, most miRNAs previously associated with HCV replication, innate interferon signaling, and hepatic fibrosis did not change significantly.  Conclusions: Changes in the host IFN-response during DAA therapy associate with favorable treatment outcome regardless of composition and duration of therapy or extent of hepatic fibrosis.

overall_design: Paired liver biopsy of pretreatment (PRE) versus end of treatment (EOT)

first: E

middle: G

last: Meissner

first: A

last: Kohli

first: K

last: Virtaneva

first: D

first: C

last: Martens

last: Porcella

first: J

last: McHutchison

first: H

last: Masur

last: Kottilil


title: In utero exposure to maternal smoking is associated with DNA methylation alterations and reduced neuronal content in the developing fetal brain

status: Public on Feb 19 2017

city: Camperdown

first: Zac

last: Chatterton

state: Australia

address: 97 Mallet St, ME30K

department: Brain and Mind Centre

country: Australia

institute: The University of Sydney

summary:
Background; Intrauterine exposure to maternal smoking is linked to impaired executive function and behavioral problems in the offspring. Maternal smoking is associated with reduced fetal brain growth and smaller volume of cortical grey matter in childhood, indicating that prenatal exposure to tobacco may impact cortical development and manifest as behavioral problems. Cellular development is mediated by changes in epigenetic modifications such as DNA methylation, which can be affected by exposure to tobacco.
Results: In this study we sought to ascertain how maternal smoking during pregnancy affects global DNA methylation profiles of the developing dorsolateral prefrontal cortex (DLPFC) during the second trimester of gestation. When DLPFC methylation profiles (Illumina, HM450) of smoking-exposed and unexposed fetuses were compared, no differentially methylated regions (DMRs) passed false discovery correction (FDR ² 0.05). However, the most significant DMRs were hypomethylated CpG Islands within the promoter regions of GNA15 and SDHAP3 of smoking-exposed fetuses. Furthermore, developmental up-regulation of SDHAP3 mRNA was delayed in smoking- exposed fetuses. DMRÕs passing FDR were found by interaction analysis between gestational age and smoking exposure annotated to SYCE3, C21orf56/LSS, SPAG1 and RNU12/POLDIP3. Utilizing established methods to estimate cell proportions by DNA methylation, we found that exposed DLPFC samples contained a lower proportion of neurons in samples from fetuses exposed to maternal smoking. We further showed that nicotine impedes the differentiation of neurons in vitro independent of cell death.
Conclusions; We found evidence that intrauterine smoking exposure alters the developmental patterning of DNA methylation and gene expression and is associated with reduced mature neuronal content, effects that are likely driven by nicotine.

overall_design: The Illumina Infinium HM450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 480,000 CpGs in 24 fetal samples dissected from the cortical plate in the region that becomes the DLPFC in order to obtain post-migratory NeuN-immunoreactive (NeuN+) neurons in the second trimester of gestation. Samples include 10 fetal cortical sections from mothers with no reported smoking prior to or during pregnancy and 14 fetal cortical sections from mothers that reported smoking prior to and during pregnancy. Genomic DNA was extracted using the QIAamp DNA Mini Kit (Qiagen) following standard instructions and bisulfite converted (Zymo). Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

first: Brigham

last: Hartley

first: Seok

last: Man-Ho

first: Natalia

last: Mendelev

first: Sean

last: Chen

first: Maria

last: Milekic

first: Gorazd

last: Rosoklija

first: Aleksander

last: Stankov

first: Iskra

last: Trencevsja-Ivanovska

first: Kristen

last: Brennand

first: Yongchao

last: Ge

first: Andrew

last: Dwork

first: Fatemeh

last: Haghighi


title: A common promoter hypomethylation signature in invasive breast, liver and prostate cancer cell lines reveals novel targets involved in cancer invasiveness

city: Montreal

first: David

last: Cheishvili

state: Quebec

address: 3655 Sir William Osler

institute: McGill

type:
Expression profiling by array
Methylation profiling by array


title: The COLCATS study: Identification of an anti-apoptotic druggable target signature for the treatment of colorectal cancer

city: Illkirch/Strasbourg

first: Wolfgang

last: Raffelsberger

address: 1 rue Laurent Fries

department: DBGS

institute: IGBMC

type:
Expression profiling by array
Third-party reanalysis

summary:
This study investigates the correlation between gene overexpression and resistance to apoptosis and hyper-proliferative phenotype in colorectal cancer.
We analyzed the transcriptome of a cohort of xenografted colorectal tumors and primary resected biopsies together with normal tissue datasets and identified a set of genes overexpressed in colon cancer.
KEYWORDS: transcription-profile, colon, colon-cancer, xenograft

overall_design: In total 203 samples (101 new samlpes plus 102 samples already on GEO) were analyzed, they represent 4 different types : colon cancer, colon cancer mouse xenograft, colon cancer cell line, and normal colon.

first: Laurent

last: Brino

first: Benoît

last: Fischer

first: Pierre

last: Kitchener

first: Armin

last: Maier

first: Gerhard

last: Kelter

first: Mourad

last: Benallaoua

first: Eric

last: Guérin

first: Florence

last: Gross

first: Agnès

last: Neuville

first: Dominique

last: Guénot

first: Marie-Pierre

last: Gaub

first: Audrey

last: Laroche-Clary

first: Valérie

last: Le Morvan

first: Olivier

last: Poch

first: Philippe

last: Bachelier

first: Loic

last: Cerf

last: Oudet

first: Heinz-Herbert

last: Fiebig

first: Jacques

last: Robert


title: Genomic, epigenomic, and transcriptomic profiling towards identifying omics-features and specific biomarkers that distinguish uterine leiomyosarcoma and leiomyoma at molecular levels

city: Fukuoka

first: Tomoko

last: Miyata

state: Fukuoka

address: 3-1-1 Maedashi, Higashi-ku

department: Gynecology and Obstetrics

institute: Kyushu University


title: Potential roles of DNA methylation in the initiation and establishment of replicative senescence revealed by array-based methylome and transcriptome analyses

status: Public on Feb 12 2017

city: Setagaya-ku

first: Mizuho

last: Sakaki

state: Tokyo

department: Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development


title: DNA methylation analysis of hepatocellular carcinoma with portal vein tumor thrombosis

status: Public on Feb 17 2017

city: Beijing

first: Jin

last: Gu

address: FIT Building 1-112C

department: Automation

institute: Tsinghua University

summary: Portal vein tumor thrombosis is a strong poor indication of HCC. Characterizing the molecular alterations of these metastatic HCCs is important for understanding the molecular mechanisms during HCC progression and metastasis. Previous genomic studies mainly focus on single molecular layer, such as gene expressions or exonic mutations. In this study, we systematically examined the copy number variation (CNV), DNA methylation, miRNA and transcriptome of matched adjacent normal tissues, primary tumors and PVTTs from 19 HCC patients. Based on the integrative multi-omics profiles, we established the molecular landscape of the metastatic HCCs and identified a set of the recurrent genomic alterations and candidate driver genes.

overall_design: Illumina Infinium HumanMethylation450 BeadChip of matched adjacent normal, primary tumor and PVTT samples from HCC patients

first: Gu

last: Jin

first: Chen

last: Lei


title: Human Alopecia Areata Skin Biopsy Samples

city: Iowa City

first: Ali

last: Jabbari

state: IA

address: 200 Hawkins Dr, 40025 PFP

institute: University of Iowa

summary:
Gene expression profiling of scalp skin biopsies from patients with alopecia areata or normal healthy controls
Scalp skin punch biopsies were taken from the indicated patients and stored in PAXgene tissue containers for shipping to a central location, where the samples were processed

overall_design: AAP (patchy type disease, n=22 patients; lesional samples n=22, nonlesional samples n=20), AAP.T (transient patchy type disease, disease duration less than 1 year, n=6; lesional samples n=6, nonlesional samples n=6), AU (alopecia universalis, n=23 patients), AT (alopecia totalis, n=9 patients), Normal (healthy controls, n=36 patients)

first: Jane

middle: E

last: Cerise

first: Angela

last: Christiano


title: Potential roles of DNA methylation in the initiation and establishment of replicative senescence revealed by array-based methylome and transcriptome analyses [methylation 450K]

summary: Cellular senescence is classified into two types; replicative and premature senescence. Gene expression and epigenetic changes are different in types of senescence, replicative and premature senescence, and cell types.  Normal human diploid fibroblast TIG-3 cells were often used in cellular senescence research, however, their epigenetic profiles were not fully understood. To elucidate how cellular senescence is epigenetically regulated in TIG-3 cells, we analyzed gene expression and DNA methylation profiles among three types of senescent cells, namely, replicative senescent, RAS-induced senescent (RIS) and non-permissive temperature-induced senescent SVts8 cells, using gene expression and methylation microarrays.   The expression of genes involved in cell cycle and immune response were commonly either down- or up-regulated among three types of senescent cells, respectively. The sequential alteration of DNA methylation level was observed only in replicative senescent cells in a time-dependent manner, but not in premature senescent cells. The integrated analysis of gene expression and methylation in replicative senescent cells demonstrated that the expression of 759 genes involved in cell cycle and immune response was associated with methylation. Furthermore, hypomethylation occurred at non-CpG island regions (open sea) on the genes with increased expression as well as non-CpG promoter of the genes related to immune response. Several miRNAs regulated by DNA methylation were found to affect the expression of their target genes. Taken together, these results indicate that DNA methylation contributes to introduction and establishment of replicative senescence partly by regulating gene expression.

overall_design: We examined the gene expression and epigenetic difference following senescence among three different types of senescent cells, replicative senescent, RAS-induced senescent (RIS) and senescent SVts8 cells, derived from Normal human diploid fibroblast TIG-3 cells. Gene expression and genome-wide DNA methylation profiles were obtained using SurePrint G3 Human GE microarray 8×60K Ver. 2.0 (Agilent) and Infinium HumanMethylation27/450 BeadChip (Illumina), respectively.

first: Yukiko

last: Ebihara

first: Kohji

last: Okamura

first: Kazuhiko

last: Nakabayashi

first: Kenichiro

last: Hata

first: Yoshiro

last: Kobayashi

first: Kayoko

last: Maehara


title: Expression data from HeLa cells treated with collismycin A

city: Wako

first: Makoto

last: Muroi

state: Saitama

department: Chemical Biology Group

institute: RIKEN CSRS

summary: Collismycin A is a microbial product. We used microarrays to examine the effect of collismycin A on gene expression of HeLa cells.

overall_design: HeLa cells were treated with collismycin A or DMSO for 18h for RNA extraction and hybridization on Affymetrix  microarrays. For comparison, Dp44mT-treated HeLa cells were also prepared.

last: Kawatani

first: Hiroyuki

last: Osada


title: Differential methylation analysis in human whole blood DNA from healthy smokers and non-smokers

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

summary: To better characterize smoking–associated methylation changes in whole blood, we used Illumina HumanMethylation450 BeadChip to assess DNA samples from current (SM, n=172) and never smokers (NS, n=81).

overall_design: 253 individual study participants consisting of 172 smokers and 81 non-smokers enrolled between 1993 and 1995 as healthy volunteers from the general public in Durham and Chapel Hill, North Carolina . These subjects were part of a community-based sample comprised of 294 healthy unrelated blacks and whites and have been described in several studies (Jones et al. 1993; Bell et al. 1995; Li et al. 2000; Lunn et al. 1999). All non-smokers were self-reported as not having smoked >100 cigarettes in their lifetime. Smokers reported their average daily cigarette consumption for the past 3 months.   The analysis of samples was carried out under an approved human subject protocol (NIEHS 86-E-0037). Nucleated DNA from whole blood was collected after sucrose-induced osmotic lysis of cells followed by phenol-chloroform extraction and DNA was stored in Tris-EDTA buffer at -20°C. The Human Methylation 450 BeadChip (Illumina) was used to measure methylation by the NCI Center for Genome Research. Specifically, 500 ng of DNA was bisulfite converted using the EZ-DNA Methylation kit (Zymo Research), hybridized to HumanMethylation450 BeadChip arrays and then scanned with an iScan microarray scanner (Illumina) following the manufacturer’s protocols. The ChAMP pipeline was used to extract and Normalize data from iDat files (Morris et al. 2014).

first: Douglas

last: Bell

first: Gary

last: Pittman

first: Michelle

last: Campbell

first: Dan

last: Su


title: The Polycomb group protein L3MBTL1 represses a SMAD5-mediated transcriptional program in human pluripotent stem cells

city: New York

first: Jeffrey

last: Zhao

state: NY

address: 1275 York Avenue

department: Genomics Core

institute: Memorial Sloan Kettering Cancer Center

summary:
Epigenetic regulation of key transcriptional programs is a critical mechanism that controls hematopoietic development and thus aberrant expression patterns or mutations in epigenetic regulators occur frequently in hematologic malignancies. We demonstrate that the Polycomb protein L3MBTL1, which is monoallelically deleted in 20q- myeloid malignancies, represses the ability of stem cells to drive hematopoietic-specific transcriptional programs by regulating the expression of SMAD5 and impairing its recruitment to target regulatory regions. Indeed, knock-down of L3MBTL1 promotes the development of hematopoiesis and impairs neural cell fate in human pluripotent stem cells. We also found a role for L3MBTL1 in regulating SMAD5 target gene expression in mature hematopoietic cell populations, thereby affecting erythroid differentiation. Taken together, we have identified epigenetic priming of hematopoietic-specific transcriptional networks, which may assist in the development of therapeutic approaches for patients with anemia.
The Polycomb protein L3MBTL1, deleted in 20q- myeloid malignancies, plays a regulatory role during differentiation of human iPS cells. Upon lentiviral knock-down of L3MBTL1, iPS cells stay poised for hematopoietic development and up-regulate expression of BMP/SMAD targets, which may also mediate impaired neural development.

overall_design: Human iPS cells at an undifferentiated stage of differentiation were lentivirally infected to express shRNAs targeting L3MBTL1. GFP+ cells were FACS sorted and subjected to RNA extraction and hybridized to Affymetrix U133plus 2.0 arrays, scanned, and subjected to quality control parameters. The data were normalized using MAS5.0.

first: Fabiana

last: Perna


title: Macrophages confer survival signals via CCR1-dependent translational MCL-1 induction in chronic lymphocytic leukemia.

first: Perry

last: Moerland

address: Meibergdreef 9

department: Epidemiology and Data Science

institute: Amsterdam UMC

summary: Protective interactions with bystander cells in micro-environmental niches such as lymph nodes (LNs) contribute to survival and therapy resistance of chronic lymphocytic leukemia (CLL) cells. This is caused by a shift in expression of BCL-2 family members. Pro-survival proteins BCL-XL, BFL-1, and MCL-1 are upregulated by LN-residing T cells through CD40L interaction, presumably via NF-κB signaling. Macrophages also reside in the LN, and are assumed to provide important supportive functions for CLL cells. However, if and how macrophages are able to induce survival is incompletely known. We first established that macrophages induced survival due to an exclusive upregulation of MCL-1. Next, we investigated the mechanism underlying MCL-1 induction by macrophages in comparison with CD40L. Genome-wide expression profiling of in vitro macrophage- and CD40L-stimulated CLL cells indicated activation of the PI3K-AKT-mTOR pathway, which was confirmed in ex vivo CLL LN material. Inhibition of PI3K-AKT-mTOR signaling abrogated MCL-1 upregulation and survival by macrophages as well asCD40 stimulation. MCL-1 can be regulated at multiple levels, and we established that AKT leads to increased MCL-1 translation, but does not affect MCL-1 transcription or protein stabilization. Furthermore, among macrophage-secreted factors that could activate AKT, we found that induction of MCL-1 and survival critically depended on C-C Motif Chemokine Receptor-1 (CCR1). In conclusion, this study indicates that two distinct micro-environmental factors, CD40L and macrophages, signal via CCR1 to induce AKT activation resulting in translational stabilization of MCL-1, and hence can contribute to CLL cell survival.

overall_design:
Patient material was obtained from three CLL patients, after written informed consent, during routine follow-up or diagnostic procedures at the Academic Medical Center, Amsterdam, the Netherlands. Peripheral blood mononuclear cells (PBMCs) of these CLL patients were isolated and stored in liquid nitrogen. Monocyte derived macrophages were obtained by differentiating monocytes isolated from healthy donor buffy coats after obtaining written informed consent. Monocytes were then differentiated to either M1 macrophages using 10ng/mL IFN-γ or M2 macrophages using 10ng/mL IL-4. NIH-3T3 mouse embryofibroblasts (3T3 cells) were supplied and characterized (for identity control, cytogenetics, and immunophenotype) by the Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ, Braunschweig, Germany). To mimic T cell induced CD40 signaling, these 3T3 cells were stably transfected with human CD40L (3T40 cells). CLL samples (n=3) were thawed and diluted and, in two different experiments, stimulated for 16h with either 3T40 cells or macrophages (M1/M2) or left untreated (CTRL). CLL cells were sorted to >99% purity using CD5/CD19 staining and FACS. Total cellular RNA was isolated and gene expression levels were measured using Affymetrix Human Genome U133 Plus 2.0 arrays.

This study includes two re-analyzed samples (CLL_CD40L_3T40_rep2; CLL_CD40L_3T40_rep3) available in the GEO database as GSE50572 (GSM1223755 and GSM1223743, respectively).

The complete dataset representing (1) 13 new samples and (2) the re-analyzed data of GSM1223755 and GSM1223743, is linked below as a supplementary file.
The results_combined.xlsx contains the results of the differential expression analysis.
The metadata.txt contains additional annotations for the re-analyzed samples (e.g. patient ID no. etc.).

first: Martijn

last: van Attekum

first: Arnon

last: Kater

first: Eric

last: Eldering


title: mRNA expression profiling of nasopharyngeal carcinoma

city: Changsha

first: Wei

last: Xiong

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

summary: Nasopharyngeal carcinoma is an Epstein-Barr virus-associated epithelial cancer with high prevalence in Southeast Asia. mRNA expression levels were measured for essentially all human genes in nasopharyngeal carcinoma tissue samples and normal nasopharyngeal tissues. Data were analyzed for differential gene expression between tumor and normal tissue.

overall_design: Total RNA extracted from laser-captured epithelium from 12 nasopharyngeal carcinomas and 4 normal healthy nasopharyngeal tissue specimens.

first: Zhaoyang

last: Zeng

first: Guiyuan

last: Li


title: Smoking-mediated Up-regulation of GAD67 Expression in the Human Airway Epithelium

first: Yael

last: Strulovici-Barel

address: 1300 York Avenue

department: Department of Genetic Medicine

institute: Weill Cornell Medical College

summary: Gamma-aminobutyric acid (GABA) is a multifunctional mediator that functions as a neurotransmitter in the central nervous system and a trophic factor during nervous system development, affecting proliferation, differentiation and cell death [1-3].GABA is synthesized from glutamate, catalyzed by GAD65 and GAD67, glutamic acid decarboxylase {Tillakaratne, Medina-Kauwe, et al. 1995 21 /id}{Owens & Kriegstein 2002 3 /id}{Watanabe, Maemura, et al. 2002 73 /id}. In the CNS transporters and catabolic enzymes work in a coordinated fashion to control the availability of GABA {Tillakaratne, Medina-Kauwe, et al. 1995 21 /id}{Owens & Kriegstein 2002 3 /id}{Watanabe, Maemura, et al. 2002 73 /id}   It is now recognized that GABA also functions in a variety of organs outside of the CNS [1,3,4]. In the lung, a series of recent studies suggest that the GABAergic signaling system plays a role in the control of asthma related-airway constriction and mucin secretion [5-9].   In the context that goblet cell hyperplasia and mucin overproduction is associated with cigarette smoking [10-12], we hypothesized that components of the GABAergic system may also be altered in the airway epithelium of cigarette smokers. To assess this hypothesis, we evaluated the expression of the entire GABAergic system in the large and small airway epithelium of healthy nonsmokers and healthy smokers. The data demonstrates there is expression of genes for a complete GABAergic system in the airway epithelium. Interestingly, the expression of GAD67 was markedly modified by smoking, with increased expression in healthy smokers compared to healthy nonsmokers at the mRNA and protein levels. In the context that mucus overproduction is commonly associated with cigarette smoking, GAD67 may be a pharmacologic target for treatment of smoking-related disorders.

overall_design: Affymetrix arrays were used to assess the expression of GAD67 gene expression data in large airway and small airway epithelium obtained by fiberoptic bronchoscopy of 21 healthy non-smokers and 31 healthy smokers (large airways) and 47 healthy non-smokers and 58 healthy smokers (small airways).

first: Gouqing

first: Rui

first: Barbara

last: Ferris

first: Jacqueline

last: Salit

first: Neil

middle: R

last: Hackett

first: Ronald

last: Crystal


title: Effect of tenascin C on brain tumor initiating cells

status: Public on Feb 08 2017

city: Calgary

first: Voon

middle: Wee

last: Yong

state: Alberta

address: 3330 Hospital drive NW

department: Clinical Neurosciences

institute: University of Calgary

summary: We have determined that tenascin C (TNC) regulates the growth of human brain tumor initiating cells (BTICs). We have identified novel mechanisms by which TNC regulates BTIC growth. Analysis of the array data identified a number of genes that were altered with TNC treatment that could potentially regulate BTIC growth. The study provides the mechanistic basis for the regulation of BTIC growth with TNC.

overall_design: We subjected one BTIC line to microarray analysis to identify genes involved in the regulation of BTIC growth. To determine the effect of TNC on BTIC gene expression, BTIC cells (BT025 cells) were treated with TNC for 6h and subjected to microarray analysis. Three (3) control and 3 treatment (TNC treated) samples were generated from BT025 line. Thus, a total of 6 RNA samples from BT025 line were obtained for microarray analysis.

first: V

first: Susobhan

last: Sarkar

first: Reza

last: Mirzaei


title: Expression data from glioblastoma tissue and normal brain tissue samples (from epilepsy surgery)

city: Guangzhou

first: YE

last: SONG

state: Guangdong

address: 1838 Guangzhoudadaobei Road

department: Department of Neurosurgery

institute: Nanfang Hospital, Southern Medical University

summary:
The characterization of glioblastoma has provided invaluable data related to this molecularly heterogeneous disease. Recent advances in high-throughput microarrays have received extensive attention and made substantial progress in reconstructing the gene regulatory network of medical biology. Using microarray analysis, significant differences in gene expression between normal and disease tissues have been observed. However, as a result of the underlying shortcomings of microarray technology, such as small sample size, measurement error, and information insufficiency, unveiling this disease mechanism has remained a major challenge to glioblastoma research. Hence, GO, pathway information, network-based approaches and machine learning algorithms have been employed to identify the mechanisms underlying this disease.
We identified the differentially expressed genes (DEGs) between 9 glioblastoma samples and 9 normal brain samples.

overall_design: The datasets available in this analysis contained 18 samples, including 9 glioblastoma tissue samples and 9 normal brain tissue samples from epilepsy surgery. All specimens had confirmed pathological diagnosis and were classified according to the World Health Organization (WHO) criteria. All the tumor samples were obtained from primary surgery. All the tissue were collectd for RNA extraction and hybridization on Affymetrix microarrays, and for other analysis.

first: Songtao

last: Qi

first: Ye

last: Song


title: Association between genome-wide DNA methylation and all-cause mortality in nonagenarians

city: University of Tampere

first: Laura

middle: Eeva Marketta

last: Kananen

state: Pirkanmaa

address: Biokatu 6

department: Department of Microbiology and immunology

country: Finland

institute: University of Tampere/School of Medicine

summary: Changes in the DNA methylation (DNAm) landscape have been implicated in aging and cellular senescence. To unravel the role of specific DNAm patterns in late-life survival, we performed genome-wide methylation profiling in nonagenarians (n=111) and determined the performance of the methylomic predictors and conventional risk markers in a longitudinal setting. The survival model containing only the methylomic predictors was superior in terms of predictive accuracy compared with the models containing the conventional predictors body mass index and mini-mental state examination. At the 2.55-year follow-up, we identified 19 mortality-associated (false-discovery rate <0.5) CpG sites that mapped to genes functionally clustering around the nuclear factor kappa B (NF-κB) complex. Interestingly, none of the mortality-associated CpG sites overlapped with the established aging-associated DNAm sites. Our results are in line with previous findings on the role of NF-κB in controlling animal life spans and demonstrate the key role of this complex in human longevity.

overall_design: Bisulphite converted DNA from 122 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Juulia

last: Jylhävä

first: Jani

last: Raitanen

first: Saara

last: Marttila

first: Tapio

last: Nevalainen

first: Marja

last: Jylhä

first: Antti

last: Hervonen

first: Mikko

last: Hurme