title: MicroRNA expression data from lymphoblastoid cell lines from patients with bipolar disorder

status: Public on Jul 04 2017

city: Paris

first: Jeverson

last: Moreira

address: 4 Avenue de l'Observatoire

country: France

institute: INSERM

summary:
Bipolar disorder (BD) (1% of the general population) is a major affective disorder characterized by recurrent manic and depressive episodes and associated with considerable burden and costs. Lithium (Li) is the first line treatment for relapse prevention in bipolar disorders with many patients who remain asymptomatic for several years (even decades). In addition, it is the only psychoactive drug that has demonstrated efficacy in suicide prevention. However a large proportion of patients is experiencing very high relapse rates (overall between 70 and 80% relapse, 2 years after a major episode).  Li mechanism of action is rather complex and still not fully understood despite extensive studies. In order to explore potential lithium effects on global gene and miRNAs expression, we initiated a study in cell-lines from excellent responders (ER) and non-responders (NR) bipolar patients
Briefly, long-term treatment response to lithium was evaluated using a validated scale “Retrospective Criteria of Long-Term Treatment Response in Research Subjects with Bipolar Disorder” , also known as the Alda scale. In our sample we analyzed dichotomous phenotypes for lithium response:  patients with total score (TS) higher or equal to 7, characterized as ER; and  patients with TS lower than 2, characterized as NR according to the literature.

overall_design: The study was performed in lymphoblastoid cell-lines (LCL) form BD patients recruited among French Centre Expert Bipolaire Network. LCLs from ER (n=4) and NR (n=4) were incubated for 4 days with or without LiCl (1mM) and microRNA profiling using Affymetrix™ microarrays was performed.

first: Cindie

last: Courtin

first: Nicolas

last: Cagnard

first: Pierre

last: Geoffroy

first: Emmanuel

last: Curis

first: Bellivier

last: Frank

first: Cynthia

last: Marie-Claire


title: MicroRNA Expression data from formalin-fixed, paraffin-embedded (FFPE) granulosa cell tumour (GCT) tissue samples

status: Public on Jul 20 2017

city: Auckland

first: Wei-Tzu

last: Cheng

address: 85 Park Road

department: Obstetrics and Gynaecology

country: New Zealand

institute: The University of Auckland

summary: Granulosa cell tumours (GCTs) of the ovary are a unique subset of ovarian stromal tumours accounting for approximately five percent of all ovarian malignancies. Based on their pathologic characteristics and clinical features, GCTs can be further divided into two distinct subtypes: adult-GCTs and juvenile-GCTs. In this study, we investigate the use of microRNAs (miRNAs) as potential biomarkers for the diagnosis and prognostication of GCTs.

overall_design: Total RNA was extracted from five adult-GCT and five juvenile-GCT FFPE tumours and hybridised on Affymetrix miRNA microarrays.

first: R

last: Rosario

first: W

middle: T


title: Genome-wide analysis of long noncoding RNA (lncRNA) expression for SAEC after treatment with demethylatiog agent (5-aza-dC) and histone deacetylase inhibitor (TSA)

status: Public on Jun 28 2017

city: Los Angeles

first: Masafumi

last: Horie

address: 2011 Zonal Ave

country: USA

institute: University of Southern California

summary: To assess transcriptional regulation by DNA demethylation in SAEC, we carried out a microarray analysis of SAEC treated with a demethylating agent (5-aza-dC) and a HDAC inhibitor (TSA). We used the Agilent SurePrint G3 Human Gene Expression 8x60K v3 microarray which contains probes for 26,083 Entrez genes and 30,606 lncRNAs.

overall_design: SAECs were treated with 3 μg/ml of 5-aza-dC on day1, 3 and 1 μg/ml of TSA on day4. Total RNA was extracted on day5, and microarray analysis was carried out using Agilent SurePrint G3 Human Gene Expression 8x60K v3.

first: Akira

last: Saito


title: Gene expression profiling of nasal epithelial cells in current and former smokers with and without lung cancer

status: Public on Jun 27 2017

city: Boston

first: Joseph

last: Perez-Rogers

state: MA

address: 72 East Concord St

department: Bioinformatics

institute: Boston University

summary: We previously derived and validated a bronchial epithelial gene expression biomarker to detect lung cancer in current and former smokers. Given that bronchial and nasal epithelium gene expression is similarly altered by cigarette smoke exposure, we sought to determine if cancer-associated gene expression might also be detectable in more readily accessible nasal epithelium. Nasal epithelial brushings were prospectively collected from current and former smokers with pulmonary lesions suspicious for lung cancer in the AEGIS-1 (n=375) and AEGIS-2 (n=130) clinical trials and gene expression profiled using microarrays. Using the 375 AEGIS 1 samples, we identified 535 genes that were differentially expressed in the nasal epithelium of patients who were ultimately diagnosed with lung cancer vs. those with benign disease after one year of follow-up (p<0.001). Using bronchial gene expression data from 299 AEGIS-1 patients (including 157 patients with matched nasal and bronchial expression data), we found significantly concordant cancer-associated gene expression differences between the two airway sites (p<0.001).  Differentially expressed genes were enriched for genes associated with the regulation of apoptosis, mitotic cell cycle, and immune system signaling. A nasal lung cancer classifier derived in the AEGIS-1 cohort that combined clinical factors and nasal gene expression had significantly higher AUC (0.80) and sensitivity (0.94) over a clinical-factor only model (p<0.05) in independent samples from the AEGIS-2 cohort (n=130). These results suggest that the airway epithelial field of lung cancer-associated injury in current and former smokers extends to the nose and demonstrates the potential of using nasal gene expression as a non-invasive biomarker for the detection of lung cancer.

overall_design: mRNA gene expression from 505 nasal epithelial brushings was profiled using Affymetrix Gene 1.0 ST microarrays. Samples were collected from patients in the Airway Epithelial Gene Expression in the Diagnosis of Lung Cancer (AEGIS) trials (AEGIS-1 and AEGIS-2), two independent, prospective, multicenter, observational studies. 375 nasal samples (243 with lung cancer, 132 with benign lung disease) were patients in the AEGIS-1 trial and 130 nasal samples (66 with lung cancer, 64 with benign lung disease) were from patients in the AEGIS-2 trial.

middle: F


title: Ammonium tetrathiomolybdate treatment targets the copper transporter ATP7A in cisplatin-resistant breast cancer TM and cisplatin sensitize resistant breast cancer.

status: Public on Jun 19 2017

city: Bethesda

first: WeiPing

last: Chen

state: MD

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

department: GCL

institute: NIDDK/NIH

summary: Chemotherapy resistance presents a major hurdle for cancer treatment. We proposed to identify the molecular changes through which breast cancer cells evolve resistance to conventional treatment, here cisplatin, so targeted therapy can be developed. Candidate approach RNAi screening was combined with cisplatin treatment in order to identify molecular pathways conferring survival advantages. The screening identified ATP7A, a copper transport ATPase responsible for the intercellular movement and sequestering of cisplatin, as a therapeutic target. Copper chelation with tetrathiomolybdate (TM) targets ATP7A. TM in combination with cisplatin sensitized drug-resistant breast cancer cells. Allograft and xenograft models in aythymic mice treated with TM/cisplatin combination therapy inhibited tumor growth and increased survival compared with monotreated mice. Examination of the molecular effects of TM on cisplatin efficacy in drug-resistant tumors revealed reduced levels of APT7A, reduced cisplatin sequestering by ATP7A and increased nuclear availability of cisplatin. Further, we showed that TM treatment combined with cisplatin reduced the half-life of ATP7A in human breast cancer cell lines. This finding offered the potential to combat drug platinum-resistant tumors and sensitize patients to conventional breast cancer treatments by identifying and targeting resistant tumors’ unique molecular adaptations.

overall_design: Three replications were treated with drugs TM, Cisp and the combined of two drugs in 12 or 24 hours with three control sample with no treatment.

first: Cristine

middle: L

last: Chisholm

first: Ada

last: Wong

first: Haitao

last: Wang

first: Guelaguetza

last: Vazquez-Ortiz

first: Weiping

first: Leigh

last: Samsel

first: Xiaoling

last: Xu

first: Chu-Xia

last: Deng


title: Expression data from proliferating and senescent IMR90 cells

status: Public on Jun 18 2017

city: Regensburg

first: Stefan

last: Dillinger

address: Universitätsstr. 31

country: Germany

institute: University Regensburg

summary: Total RNA was isolated from proliferating and senescent IMR90 cells to compare gene-expression to the changes in nucleolus-association in proliferating and senescent IMR90 cells.

overall_design: IMR90 cells were grown in standard medium and RNA was isolated from proliferating cells. Then cells were grown until senescence (stop of proliferation, positive beta-galactosidase test) and total RNA was again isolated.

first: Attila

last: Németh


title: PI3K/AKT/mTOR and Sonic hedgehog pathways cooperate together to inhibit human pancreatic cancer stem cell characteristics and tumor growth

city: Kansas City

first: Sumedha

last: Gunewardena

state: Kansas

address: 3901 Rainbow Boulevard

institute: University of Kansas Medical Center

summary: Cancer stem cells (CSCs) play major roles in cancer initiation, progression, and metastasis.  It is evident from growing reports that PI3K/Akt/mTOR and Sonic Hedgehog (Shh) signaling pathway are aberrantly reactivated in pancreatic CSCs.  Here, we examined the efficacy of combining NVP-LDE-225 (PI3K/mTOR inhibitor) and NVP-BEZ-235 (Smoothened inhibitor) on pancreatic CSCs characteristics, microRNA regulatory network, and tumor growth.  NVP-LDE-225 cooperated with NVP-BEZ-235 in inhibiting pancreatic CSC’s characteristics and tumor growth in NOD/SCID IL2R null mice by acting at the level of Gli.  Combination of NVP-LDE-225 and NVP-BEZ-235 inhibited self-renewal capacity of CSCs by suppressing the expression of pluripotency maintaining factors Nanog, Oct-4, Sox-2 and cMyc.  NVP-LDE-225 cooperated with NVP-BEZ-235 to inhibit Lin28/Let7a/Kras axis in pancreatic CSCs.  Furthermore, synergistic interaction of these drugs was observed on spheroid formation by pancreatic CSCs isolated from Pankras/p53 mice.  The combination of these drugs also showed synergistic effects on the expression of proteins involved in cell survival and apoptosis.  In addition, synergistic effects of these drugs were observed on inhibition of epithelial-to-mesenchymal transition (EMT) through modulation of cadherin, vimentin and transcription factors Snail, Slug and Zeb1.  In conclusion, these data suggest that the combined inhibition of PI3K/Akt/mTOR and Shh pathways may be an effective strategy for the treatment of pancreatic cancer.

overall_design: Pancreatic CSCs were treated with NVP-BEZ-235 (1 µM) and NVP-LDE-225 (5 µM) in duplicate for 36 h.  RNAs were isolated using the trizol reagent (invitrogen, CA, USA).  The expression levels of expressed miRNAs were measured using Affymetrix GeneChip miRNA 3.0 arrays. Only probesets of human small-RNAs in the array were used for the analysis.

first: Narinder

last: Sharma

first: Rajesh

last: Nanta

first: Jay

first: Sharmila

last: Shankar

first: Rakesh

middle: K

last: Srivastava


title: Comparison of global gene expression between reactive and anergic human basophils after anti-FCERIA stimulation

status: Public on Jun 15 2017

first: Bernett

last: Lee

address: 8A Biomedical Grove #03-06 Immunos

country: Singapore

institute: Singapore Immunology Network

summary: Basophil functional state was determined using the Flow2CAST Basophil Activation Test (BAT). Human basophils were isolated from whole blood of three house dust mite (HDM) responsive donors with reactive basophils and two donors with anergic basophils. Basophil isolation was performed using the EasySep Human Basophil Enrichment kit (Stemcell). Purity of the basophils was determined by flow cytometry and ranged from 96 - 99%. For stimulation, 75,000 basophils were incubated for 4 hr with or without 50 ul of anti-FCERI antibody (Bühlmann Laboratories) in a total volume of 200 ul of Stimulation Buffer provided by the Flow2CAST kit. After incubation, the basophils were collected and re-suspended in TRIzol Reagent (Life Technologies). Total RNA was extracted using double extraction protocol using the guanidinium thiocyanate-phenol-chloroform extraction (Trizol Invitrogen), followed by a Qiagen RNeasy Micro clean-up procedure. cDNA and ST-ssDNA were prepared, fragmented and labeled according to Nugen WT Ovation Pico RNA Amplification and WT Ovation Exon kit and Encore Biotin protocols. The labeled ssDNA was hybridized on the Affymetrix Human GeneChip 1.0 ST Arrays, which subsequently were processed and stained using GeneChip Fluidics Station 450. The stained GeneChip Arrays were scanned in the Microarray Facility at the Biopolis Shared Facility using a GeneChip Scanner 3000. Quality control for the Arrays was performed using the Affymetrix Expression Console Software.

overall_design: Basophil functional state was determined by BAT. Purified basophils were stimulated with or without anti-FCERI monoclonal antibody. Global gene expression was performed using the Affymetrix Human GeneChip 1.0 ST Arrays.

first: Kia

middle: J

last: Puan

first: Anand

last: Andiappan

first: Dilip

last: Kumar

first: Lai

last: Siong

first: Giminna

last: Yeo

first: Derya

last: Bercin

first: Mireille

last: Starke

first: Doreen

last: Haase

first: Josephine

last: Lum

first: Fook

last: Chew

first: John

last: Connolly

first: Siew

middle: C

first: Francesca

last: Zolezzi

first: Michael

last: Poidinger

first: Wang

last: De Yun

first: Olaf

last: Rötzschke


title: Real-Time PCR analysis of Embryoid Body differentiation of Human pluripotent stem cells

status: Public on Jun 20 2017

city: Sheffield

first: Paul

last: Gokhale

address: Western Bank

department: Biomedical Science

country: United Kingdom

institute: University of Sheffield

summary: Human pluripotent stem cells were differentiated by size-controlled embryoid body (EB) formation in defined neutral, ectoderm, endoderm and mesoderm conditions.  EB's were analysed at 4, 10 and 16 days post induction by real-time PCR using the Fludigm Deltagene primers and probes.

overall_design: 575 samples (with replicates) from undifferentiated pluripotent stem cells, Embryoid body samples at day 4, 10 and 16 post induction of differnetiation, in four conditions and Teratoma samples from the same cell lines

last: Robson

first: Florian

last: Halbritter


title: Gene expression of viable human AML cells purified by FACS from bone marrows of three AML PDX treated by PBS(vehicle) or cytarabine

status: Public on Jun 25 2017

city: Strassen

first: Tony

last: KAOMA

address: 1 A-B Rue Thomas Edison

department: Quantitative Biology Unit

country: Luxembourg

institute: Luxembourg Institute of Health

summary: It has been hypothesized that chemotherapy resistant human acute myeloid leukemia (AML) cells are enriched in an immature phenotype, cellular quiescence and leukemic initiating cells (LICs). However, these hypotheses have never been validated completely in vivo. We have developed a physiologically relevant chemotherapeutic approach with cytosine arabinoside AraC using patient-derived xenograft (PDX) models. AraC-treated AML cells are not consistently enriched for either immature cells or quiescent cells. AraC treatment does not enrich for LICs as measured by limiting dilution in secondary transplantations. Rather chemotherapy resistant cells in vivo have high levels of reactive oxygen species (ROS) and a gene signature consistent with oxidative phosphorylation (OXPHOS). Treatment of human HIGH OXPHOS but not LOW OXPHOS AML cell lines showed chemotherapy resistance in vivo, showing that essential mitochondrial functions make significant contributions to AraC resistance in AML. Accordingly, targeting mitochondrial OXPHOS metabolism through the inhibition of mitochondrial protein synthesis, the electron transfer chain or fatty acid oxidation induced an energetic shift towards LOW OXPHOS and strongly enhanced anti-leukemic effects of AraC in AML cells. These results demonstrate that chemotherapy resistance in AML is not necessarily associated with stemness but is highly dependent on a distinct oxidative metabolism, and that the HIGH OXPHOS gene signature is a robust hallmark of the AraC response in PDX and a promising therapeutic avenue to treat AML residual disease.

first: Robin

last: Perry

first: Danet-Desnoyers

last: Gwenn

first: Carroll

last: Martin

first: Sarry

last: Jean-Emmanuel

first: Kaoma

last: Tony


title: Gene expression profiling of the NLPHL cell line DEV after coculture with T cells and monocytes

status: Public on Jun 12 2017

city: Frankfurt

first: Claudia

last: Döring

address: Theodor Stern Kai 7

department: Medical School, Institite of Pathology

institute: Johann Wolfgang-Goethe University Frankfurt a.M.

summary:
Nodular lymphocyte predominant Hodgkin lymphoma (NLPHL) is an indolent lymphoma, but can transform into diffuse large B cell lymphoma (DLBCL), showing a more aggressive clinical behavior. Little is known about these cases on the molecular level. Therefore, the aim of the present study was to characterize DLBCL transformed from NLPHL
(LP-DLBCL) by gene expression profiling (GEP). GEP revealed an inflammatory signature pinpointing to a specific host response. In a coculture model resembling this host response, DEV tumor cells showed an impaired growth behavior. Mechanisms involved in the reduced tumor cell proliferation included a downregulation of MYC and its target genes. Lack of MYC expression was also confirmed in 12/16 LP-DLBCL by immunohistochemistry. Furthermore, CD274/PD-L1 was upregulated in tumor cells after coculture with T cells or monocytes and its expression was validated in 12/19 cases of LP-DLBCL. Thereby, our data provide new insights into the pathogenesis of LP-DLBCL and a concrete explanation of the relatively low tumor cell content. Moreover, our results suggest that treatment of these patients with checkpoint inhibitors may enhance an already ongoing host response in these patients.

overall_design: DEV cells were MACS purified after coculture experiments with T cells and monocytes, and gene expression profiling was performed.

first: Sylvia

last: Hartmann


title: Small and big Hodgkin-Reed-Sternberg cells of Hodgkin lymphoma cell lines L-428 and L-1236 lack consistent differences in gene expression profiles and are capable to reconstitute each other

status: Public on Jun 09 2017

summary:
Gene expression analysis was performed from microdissected small and big HRS cells, which were taken from smears of the Hodgkin cell lines
L1236 and L428

overall_design: Small HRS cells (< 350µm) and big HRS cells (>600µm) were separately microdissected


title: Genexpression Profiling of DLBCL derived from NLPHL

summary: Nodular lymphocyte predominant Hodgkin lymphoma (NLPHL) is an indolent lymphoma, but can transform into diffuse large B cell lymphoma (DLBCL), showing a more aggressive clinical behavior. Little is known about these cases on the molecular level. Therefore, the aim of the present study was to characterize DLBCL transformed from NLPHL (LP-DLBCL) by gene expression profiling (GEP). GEP revealed an inflammatory signature pinpointing to a specific host response. In a coculture model resembling this host response, DEV tumor cells showed an impaired growth behavior. Mechanisms involved in the reduced tumor cell proliferation included a downregulation of MYC and its target genes. Lack of MYC expression was also confirmed in 12/16 LP-DLBCL by immunohistochemistry. Furthermore, CD274/PD-L1 was upregulated in tumor cells after coculture with T cells or monocytes and its expression was validated in 12/19 cases of LP-DLBCL. Thereby, our data provide new insights into the pathogenesis of LP-DLBCL and a concrete explanation of the relatively low tumor cell content. Moreover, our results suggest that treatment of these patients with checkpoint inhibitors may enhance an already ongoing host response in these patients.

overall_design: Gene expression from primary FFPE samples


title: Genomic characterization of liver metastases from colorectal cancer patients [miRNA-3]

city: Salamanca

first: Jose

middle: María

last: Sayagués

state: Salamanca

address: Campus Miguel de Unamuno

department: Department of Medicine

country: Spain

institute: Cancer Research Center (IBMCC-CSIC/USAL)

summary: Metastatic dissemination is the most frequent cause of death sporadic colorectal cancer (sCRC) patients. The genomic abnormalities which are potentially characteristic of such advanced stages of the disease are complex and so far, they have been poorly described and only partially understood. We evaluate the molecular heterogeneity of sCRC tumors based on simultaneous assessment of the overall GEP of both coding mRNA and non-coding RNA genes in primary sCRC tumor samples from 23 consecutive patients and their paired liver metastases. Liver metastases from the sCRC patients analyzed, systematically showed deregulated transcripts of those genes identified as also deregulated in their paired primary colorectal carcinomas. However, some transcripts were found to be specifically deregulated in liver metastases while expressed at normal levels in their primary tumors, suggesting an increased genomic instability of neoplastic cells from metastatic versus primary tumor samples. Of note, once tumoral samples were normalized vs. non-tumoral colorectal tissue, only three mRNAS (i.e.: DEFB1, COL12A and PTGER3) and one miRNA (i.e.: miR-572) emerged as significantly deregulated in the liver metastases vs. the primary tumor. Canonical pathways found to be specifically deregulated in liver metastatic samples included multiple genes related with intercellular adhesion and the metastatic processes (e.g., IGF1R, PIK3CA, PTEN and EGFR), endocytosis (e.g., the PDGFRA, SMAD2, ERBB3, PML and FGFR2), and cell cycle (e.g., SMAD2, CCND2, E2F5 and MYC). Our results also highlight the activation of genes associated with the TGFβ signaling pathway, which thereby emerge as candidate genes to play an important role in CRC tumor metastasis.

overall_design: Tissue specimens from 23 sporadic colorectal adenocarcinomas and 19 liver metastases (n=42 samples) were obtained from 23 patients with metastatic lesions susceptible of being resected (16 males and 7 females; median age of 66 years, ranging from 48 to 80 years) after informed consent had been given by each subject. The studied cases corresponded to 23 consecutive metastatic colorectal cancer patients.

first: José

middle: M

last: Sayagues

first: Luis

last: Corchete

first: María

last: Gutierrez

last: del Mar Abad

first: Oscar

last: Bengoechea

first: Encarna

last: Fermiñan

first: Maria

last: Anduaga

first: Manuel

last: Iglesias

first: Carmen

last: Esteban

last: Angoso

middle: A

last: Alcazar

first: Jacinto

last: Garcia

first: Alberto

last: Orfão

last: Muñoz-Bellvis


title: KLF family members KLF4 and KLF7 regulate corneal epithelium [siKLF7_undifferentiated]

status: Public on Jun 01 2017

city: Irvine

first: Bogi

last: Andersen

state: CA

address: 839 Health Sciences Dr.

department: Medicine

institute: University of California, Irvine

summary: While the regulatory landscape during stem cell differentiation has been well characterized, the shared and unique regulatory mechanisms in different ectodermally-derived epithelial cells have not been well described. Through defining the complement of super enhancers and typical enhancers in corneal epithelium for the first time, we show that regulatory regions are often shared between cell types of the same lineage, and that corneal super enhancers are already marked as potential regulatory domains in embryonic stem cells. Through the enrichment of KLF motifs in enhancers, we identified and defined a novel role for Kruppel family member KLF7 in promoting the corneal progenitor cell state, in many cases working antagonistically to corneal differentiation promoting KLF4. Our work highlights the importance of balance between proliferation and differentiation, both for proper tissue development and for homeostasis.

overall_design: pooled siRNA was used to knockdown KLF7 in duplicate with 2 scramble siRNA controls. RNA was extracted and submitted for microarray.

first: Rachel

last: Herndon Klein


title: Profiling of in vitro differentiated activated T helper cells

status: Public on Jun 06 2017

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

institute: Helmholtz Zentrum Muenchen

type:
Expression profiling by array
Non-coding RNA profiling by array

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: KLF family members KLF4 and KLF7 regulate corneal epithelium [siKLF4_undifferentiated]

overall_design: pooled siRNA was used to knockdown KLF4 in duplicate with 2 scramble siRNA controls. RNA was extracted and submitted for microarray.


title: Improving the Positive Predictive Value of Non-invasive Prenatal Screening (NIPS)

status: Public on May 22 2017

city: San Juan Capistrano

first: Jared

last: Taylor

address: 33608 Ortega Highway

institute: Quest Diagnostics Inc

summary: Assessment of maternal blood to detect maternal microduplication causing false positive trisomy result in fetus

overall_design:
Array evidence including 2 maternal gDNA samples which were positive for a maternal duplication on either chromosome 18 or 21
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood samples.

first: Charles

last: Strom

first: Renius

last: Owen

first: Joseph

last: Catanese


title: miRNA profiles in obese and normal weight periodontitis patients

status: Public on May 31 2017

city: London

first: Anastasia

middle: Z.

last: Kalea

address: 5 University Street

department: Centre for Cardiovascular Genetics

institute: UCL Institute of Cardiovascular Science

summary: Affymetrix GeneChip miRNA 3.0 microarrays were compared in gingival tissue biopsy samples from obese and normal weight patients with periodontitis

overall_design: Total RNA was extracted from gingival tissue biopsies (miRVana protocol) collected from normal weight and obese individuals with periodontitis. MiRNA expression profiling was performed using Affymetrix GeneChip miRNA 3.0 arrays.

middle: Z


title: Gene expression in Peyronie disease, tunica albuginea, and corpora cavernosum in cultured cells from human penis

status: Public on May 15 2017

city: Torrance

first: Robert

last: Gelfand

address: 1124 W. Carson St

department: surgery

institute: LABiomed at Harbor UCLA,  and Charles Drew Univ

summary:
Cells from normal tissues and from a Peyronie Disease plaque of human penis were cultured and RNA was extracted.
The aim was to investigate differences in gene expression in the abnormal plaque as well as to establish baseline expression data in normal tissues for comparison.

overall_design: Cells were incubated in six well plates in the presence or absence of TGFb, a known inducer of Peyronie Disease-like plaque in animal systems. RNA was extracted using Trizol reagent and the RNA was further purified for DNA microarray analysis using the Qiagen RNeasy Plus Micro kit. RNA samples were analyzed by the UCLA DNA Core using the Affymetrix human Gene 1.0 ST system. Data were normalized by the UCLA core.

first: Dolores

last: Vernet

first: Istvan

last: Kovanecz

first: Jacob

last: Rajfer

first: Nestor

last: Gonzalez-Cadavid


title: Adipocyte-derived Exosomal miRNAs from Subcutaneous Adipose Tissue: A Novel Mechanism for Obesity-Related Disease

city: Washington

last: Freishtat

state: DC

address: 111 Michigan Avenue NW

department: Center for Genetic Medicine

institute: Children's National Medical Center

summary: Affymetrix miRNA 3.0 array profiling of adipocyte-derived exosomes from obese and lean human subjects. We used miRNA arrays to profile exosomes shed from obese and lean human subcutaneous fat that was cultured for 60 minutes.

overall_design: Human obese and lean subcutaneous fat were surgically acquired, dissected, and promptly cultured for 60 minutes. We used the culture supernatants for exosome purification and isolation using ExoQuick-TC Precipitation Solution.

first: Matthew

last: Barberio

first: Evan

last: Nadler

first: Sarah

last: Ferrante


title: mRNA expression  profiles in human cervix at preterm delivery, delivery after preterm premature rupture of membranes and term delivery

city: Stockholm

first: Aurelija

last: Dubicke

address: Karolinska University Hospital Solna

department: Department of Women's and Children's Health

country: Sweden

institute: Karolinska Institutet

summary: Objective: Mechanisms of preterm labour (PTL) are not fully elucidated. Cervical ripening plays an important role. We aimed to investigate possible differences in gene expression in human cervix between PTL and term labour (TL) and between PTL and preterm premature rupture of membranes (PPROM).

overall_design: Cervical biopsies were obtained from women immediately postpartum (within 30 minutes). The biopsies were taken transvaginally with scissors and tweezers at twelve o'clock position. There were 3 women in each group (preterm labor, preterm premature rupture of membranes and term labor) included.

first: Birgitte

middle: S

last: Oxlund

first: Emma

last: Fransson

first: Birgitta

last: Byström

first: Lalit

last: Kumar

first: Gunvor

last: Ekman-Ordeberg


title: Effects of altered expression and activity levels of casein kinase 1δ and ε on tumor growth and survival of colorectal cancer patients

status: Public on May 19 2017

city: Ulm

first: Uwe

last: Knippschild

address: Albert-Einstein-Allee 23

department: General and Visceral Surgery

institute: University Hospital Ulm

summary:
Colorectal cancer (CRC) is the fourth leading cause of cancer-related death worldwide due to high apoptotic resistance and metastatic potential. Since mutations as well as deregulation of CK1 isoforms contribute to tumor development and progression, CK1 has become an interesting drug target. In this study, we show that CK1 isoforms are differently expressed in colon tumor cell lines and that growth of these cell lines can be inhibited by CK1-specific inhibitors. Furthermore, expression of CK1δ and ε is changed in colorectal tumors and high CK1ε expression levels significantly correlate with prolonged patients' survival. In addition to changes in CK1δ and ε expression, mutations within exon 3 of CK1δ were detected in colorectal tumors. These mutations influence ATP binding, leading to changes in the kinetic parameters.
Overexpression of these mutants in HT29 cells alters their ability to grow anchorage independently. Consistent with these results, these CK1δ mutants lead to differences in proliferation rate and tumor size in xenografts due to changes in gene expression, especially in genes involved in regulation of cell proliferation, cell cycle, and apoptosis. In summary, our results provide evidence that changes in the expression levels of CK1 isoforms in colorectal tumors correlate with the survival of patients and that CK1δ mutations affect growth and proliferation of tumor cells and induced tumor growth in xenografts, leading to the assumption that CK1 isoforms provide interesting targets in new colorectal cancer therapy concepts.

overall_design: To analyze the effects of the different exon 3 mutants of CK1δ on tumor cell growth and proliferation in vivo, HT29 cells stably expressing mtCK1δT67S, mtCK1δI68N, mtCK1δP66T,R69K, or the empty vector were subcutaneously injected into the hind flank of 6- to 8-week-old athymic nude mice to obtain xenografts. After 27 days, mice were sacrificed and the tumors were excised, measured, and weighed. Microarray analysis was performed to compare gene expression in the different groups (vector control group (ctrl), mtCK1δT67S, mtCK1δI68N, and mtCK1δP66T,R69K), using 200 ng total RNA as starting material and 5.5 µg ssDNA per hybridization (GeneChip Fluidics Station 450; Affymetrix, Santa Clara, CA).

first: Julia

last: Richter

first: Kalim

last: Ullah

first: Pengfei

last: Xu

first: Vanessa

last: Alscher

first: Christian

last: Peifer

first: Jakob

last: Halekotte

first: Johan

last: Leban

first: Daniel

last: Vitt

first: Karlheinz

last: Holzmann

first: Vasiliy

last: Bakulev

first: Lorenzo

last: Pinna

first: Doris

last: Henne-Bruns

first: Andreas

last: Hillenbrand

first: Marko

last: Kornmann

first: Frank

last: Leithäuser

first: Joachim

last: Bischof


title: Expression data from Human Microvascular Endothelial Cells exposed or not to low-dose ionizing radiation

city: Oeiras

first: Jorg

middle: D

last: Becker

address: Rua da Quinta Grande No 6

country: Portugal

institute: Instituto Gulbenkian de Ciencia

summary: We have previously shown that low doses of ionizing radiation (LDIR) induce angiogenesis. In the present study we investigated their action in experimentally induced hindlimb ischemia. We demonstrated that 0.3 Gy, administered for four consecutive days, significantly improves blood perfusion in the murine ischemic limb by stimulating angiogenesis and arteriogenesis. This is achieved through durable and simultaneous up-regulation of a repertoire of pro-angiogenic factors and their receptors in endothelial cells, as evident in cells isolated from the irradiated gastrocnemius muscles. Moreover, we demonstrated that this mechanism is mediated via VEGFR signaling, since VEGFR inhibition abrogated the LDIR-mediated gene up-regulation and impeded the increase in vessel density. Importantly, the vasculature in an irradiated non-ischemic bed is not affected and no adverse effects associated to the use of LDIR were seen.   These findings disclose an innovative, non-invasive strategy to induce therapeutic angiogenesis in a murine model of severe hindlimb ischemia, emerging as a novel approach in the treatment of Critical Limb Ischemia patients.

overall_design: Four RNA samples of irradiated and non-irradiated (control) Human Microvascular Encothelial Cells-Lung were processed for hybridization to Affymetrix Human Gene  1.0 ST arrays.

first: Augusto

last: Ministro

first: Paula

last: de Oliveira

first: Raquel

last: Nunes

first: André

last: Rocha

first: Adriana

last: Correia

first: Tânia

last: Carvalho

first: Pedro

last: Faísca

first: Jörg

first: João

last: O’Neill

first: Marília

last: Jorge

first: Esmeralda

last: Poli

first: Marc

last: Mareel

first: Susana

last: Santos


title: Expression data from U2OS-ER-alpha cells

status: Public on Apr 30 2017

city: Pittsburgh

first: Rebecca

middle: Jean

last: Watters

state: PA

address: 204 Craft Avenue

institute: University of Pittsburgh

summary:
Understanding the mechanism of SRC-1 dependent and independent E2 signaling in bone will provide a better understanding of the biology underlying osteoporosis.
We studied E2 and SRC-1 regulated transcriptomes to identify high confidence E2-independent and E2-dependent, SRC-1 target genes involved in important processes in bone.

overall_design: U2OS-ERα cells (supplied by TC Spelsberg, Mayo Clinic),  Cells (2 × 105) were cultured in 6-well plates in appropriate culture medium.  The cells were then transfected with 50 nM siRNA using Lipofectamine2000 (Invitrogen).  The medium was switched to IMEM + 5% CSS the next day and the cells were treated with vehicle (EtOH) or estrogen (E2) for 3 hr.  The following siRNAs were purchased from Dharmacon: ON-TARGETplus Non-Targeting pool (D-001810-10), ON-TARGETplus GSK3 SMARTpool (L-003010-00), and ON-TARGETplus SRC-1/NCOA1 SMARTpool (L-005196-00).  RNA was isolated using Qiagen RNeasy kit and run on an Affymetrix Human Gene 1.0 ST array.  Affymetrix CEL files of the microarray experiments were processed using the “affy” package and differential expression was assessed using the “limma” package of the Bioconductor Suite (http://www.bioconductor.org/). The threshold for detecting differential expression was set at p-value < 0.01 and q-value < 0.05.

first: Steffi

last: Oesterreich


title: Time-course expression data from HEK293∆RAF1:ER cells stimulated with 4OHT, U0126, CYHX, ActD, EGF, FGF, or IGF

status: Public on Apr 28 2017

city: New York

first: Florian

last: Uhlitz

state: NY

address: 1275 York Avenue

department: Computational Oncology

institute: Memorial Sloan Kettering Cancer Center

summary: We integrate experimental data and mathematical modelling to unveil how ERK signal duration is relayed to mRNA dynamics.

overall_design: HEK293 cells were transfected with an inducible form of RAF (∆RAF1:ER) and induced with tamoxifen (4OHT) or stimulated with different growth factors (EGF, FGF, iGF). Effects of RAF signalling were perturbed subsequently or in parallel with MEK inhibtor U0126, translation inhibtor cycloheximide (CYHX) and actinomycin D (ActD).

first: Nils

last: Blüthgen


title: The role of Hoxa9 and Meis1 in development of acute myeloid leukemia

status: Public on Apr 27 2017

city: Gothenburg

first: Lars

last: Palmqvist

address: Sahlgrenska University Hospital

department: Institute of Biomedicine

institute: University of Gothenburg

summary: OBJECTIVE: MEIS1, a HOX cofactor, collaborates with multiple HOX proteins, such as HOXA9, to accelerate the onset of acute myeloid leukemia (AML) through largely unknown molecular mechanisms. To further resolve these mechanisms, we conducted a structure-function analysis of Meis1 and miRNA expression profiling, in the context of Hoxa9 leukemogenesis. RESULTS: We show, in a murine bone marrow transplantation model, that the homeodomain of Meis1 is required for leukemogenic collaboration with Hoxa9. miRNA expression profiling of a Hoxa9 preleukemic cell line transduced with wild-type or Meis1 homeodomain mutant reveal deregulation of multiple miRNA including a set not previously implicated as Meis1 targets.

overall_design: Murine bone marrow cells transduced with Hoxa9-GFP + empty MIY vector were compared to Hoxa9+Meis1 cells or Hoxa9+Meis1 with deleted homeodomain (DHD) cells and cultured for three or four weeks before harvest for miRNA expression array. Four independent experiments were performed for each of the three different conditions included in the study. Cells from all samples were also transplanted into lethally irradiated mice to test for their transforming and leukemic potential.


title: Lineage specific differentiation is influenced by state of human pluripotency [human]

status: Public on Apr 26 2017

city: Hamilton

first: Mickie

last: Bhatia

state: Ontario

address: 1200 Main Street West

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

country: Canada

institute: McMaster University

summary: Human pluripotent stem cells (hPSCs) have been reported in naïve and primed states. However, the ability of human PSCs to generate mature cell types is the only imperative property for translational utility. Here, we reveal that the naïve state enhances self-renewal capacity while restricting lineage differentiation in vitro to neural default fate. Gene expression analyses indicate expression of multiple lineage associated transcripts in naïve hPSCs and thus failed to predict biased functional differentiation.  Naïve hPSCs can be converted to primed allowing recovery of multilineage differentiation over long serial passage or immediately through suppression of OCT4 but not NANOG. To this end, we identified chemical inhibitors of OCT4 expression that acutely restore naïve hPSC differentiation. Our study identifies unique cell fate features and critical restrictions in human pluripotent states, and provides an approach to overcome these barriers that harness both efficient naïve hPSC growth whilst maintaining in vitro differentiation capacities essential for hPSC applications.

overall_design: Transcriptome analysis was performed on bulk culture of PSC lines in order to compare their RNA expression profile to samples of naïve and primed PSCs from the literature

first: Jong-Hee

last: Lee


title: GRHL3 binding and the enhancer landscape are reorganized during transitions between different functional states of epidermal keratinocytes [siREST-migration]

status: Public on Apr 12 2017

first: Bogi

last: Andersen

summary: The genomic mechanisms underlying progressive, irreversible cell lineage commitments and differentiation, which include large scale chromatin re-organization, transcription factor binding, and chromatin modifications, have been well defined. However, we know little about the chromatin changes during transitions between transient cell states such as cell migration. Here we demonstrate the formation of unique complements of typical enhancers and super-enhancers as human progenitor keratinocytes either differentiate or migrate. Unique super-enhancers for each cellular state are linked to gene expression that confer functions associated with each cell state, and sequence variants associated with skin diseases are enriched within super-enhancers. GRHL3, a factor that promotes both differentiation and migration, exhibits prominent super-enhancer interactions in differentiating keratinocytes, while during migration, it preferentially binds to promoters along with REST, repressing the expression of migration inhibitors. Key epidermal differentiation transcription factor genes, including GRHL3, are located within super-enhancers, and many of these transcription factors in turn bind to and regulate super-enhancers. Of note, GRHL3 also represses the formation of a number of progenitor and non-keratinocyte super-enhancers in differentiating keratinocytes.  Thus, coordinated GRHL3 binding and enhancer rearrangements regulate the functional states of keratinocytes.

overall_design: pooled siRNA was used to knockdown REST in duplicate, with 2 scramble siRNA control replicates. Cells were induced to migrate and collected 12 hours later. RNA was extracted and submitted for microarray.

first: Rachel

last: Herndon Klein


title: MRPL53, a New Candidate Gene for Orofacial Clefting, Identified Using an eQTL Approach

status: Public on Apr 19 2017

city: Sao Paulo

first: Cibele

last: Masotti

state: São Paulo

address: Rua do Matao, 277.

department: Genetics and Evolutionary Biology

country: Brazil

institute: University of Sao Paulo

type:
Expression profiling by array
SNP genotyping by SNP array

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

A valuable approach to understand how individual and population genetic differences can predispose to disease is to assess the impact of genetic variants on cellular functions (e.g., gene expression) of cell and tissue types related to pathological states. To understand the genetic basis of nonsyndromic cleft lip with or without cleft palate (NSCL/P) susceptibility, a complex and highly prevalent congenital malformation, we searched for genetic variants with a regulatory role in a disease-related tissue, the lip muscle (orbicularis oris muscle [OOM]), of affected individuals. From 46 OOM samples, which are frequently discarded during routine corrective surgeries on patients with orofacial clefts, we derived mesenchymal stem cells and correlated the individual genetic variants with gene expression from these cultured cells. Through this strategy, we detected significant cis-eQTLs (i.e., DNA variants affecting gene expression) and selected a few candidates to conduct an association study in a large Brazilian cohort (624 patients and 668 controls). This resulted in the discovery of a novel susceptibility locus for NSCL/P, rs1063588, the best eQTL for the MRPL53 gene, where evidence for association was mostly driven by the Native American ancestry component of our Brazilian sample. MRPL53 (2p13.1) encodes a 39S protein subunit of mitochondrial ribosomes and interacts with MYC, a transcription factor required for normal facial morphogenesis. Our study illustrates not only the importance of sampling admixed populations but also the relevance of measuring the functional effects of genetic variants over gene expression to dissect the complexity of disease phenotypes.


title: GRHL3 binding and the enhancer landscape are reorganized during transitions between different functional states of epidermal keratinocytes [siGRHL3-migration]

overall_design: pooled siRNA was used to knockdown GRHL3 in duplicate, with 2 scramble siRNA control replicates collected at 0 hours, and 2 scramble control replicates collected at 12 hours. Cells were induced to migrate and collected 12 hours later (72 hours after transfection). RNA was extracted and submitted for microarray.


title: miR-204 down-regulation elicited perturbation of a gene target signature common to human cholangiocarcinoma and gastric cancer.

status: Public on Apr 10 2017

city: rome

first: andrea

last: sacconi

address: via elio chianesi

country: Italy

institute: regina elena cancer institute

summary:
There is high need of novel diagnostic and prognostic tools for tumors of the digestive system, such as gastric cancer and cholangiocarcinoma.
We employed  Affymetrix profiling of 15 gastric tumor tissues and 5 normals to evaluate the levels of miR-204 target genes. We performed extensive in silico analysis to identify a minimal gene target signature which anti-correlated with the levels of miR-204 and validated all of the findings on publicly available databases. We employed transient transfection experiments, clonogenic assays and cell cycle profiling to evaluate the dependency of the target genes signature of miR-204 and the biological consequences of miR-204 perturbation.
Then we validate the data obtained in a cohort of tumoral and normal gastric samples, tumoral and normal cholangiocarcinoma samples. to statistically strengthen the genes signature obtained we analyzed data available on gastric, colangiocarcinoma, esophageal and colon  database

overall_design: 15 gastric tumor tissues and 5 normals

first: Andrea

last: Sacconi

first: Giovanni

last: Blandino


title: MRPL53, a New Candidate Gene for Orofacial Clefting, Identified Using an eQTL Approach [expression array]

summary: A valuable approach to understand how individual and population genetic differences can predispose to disease is to assess the impact of genetic variants on cellular functions (e.g., gene expression) of cell and tissue types related to pathological states. To understand the genetic basis of nonsyndromic cleft lip with or without cleft palate (NSCL/P) susceptibility, a complex and highly prevalent congenital malformation, we searched for genetic variants with a regulatory role in a disease-related tissue, the lip muscle (orbicularis oris muscle [OOM]), of affected individuals. From 46 OOM samples, which are frequently discarded during routine corrective surgeries on patients with orofacial clefts, we derived mesenchymal stem cells and correlated the individual genetic variants with gene expression from these cultured cells. Through this strategy, we detected significant cis-eQTLs (i.e., DNA variants affecting gene expression) and selected a few candidates to conduct an association study in a large Brazilian cohort (624 patients and 668 controls). This resulted in the discovery of a novel susceptibility locus for NSCL/P, rs1063588, the best eQTL for the MRPL53 gene, where evidence for association was mostly driven by the Native American ancestry component of our Brazilian sample. MRPL53 (2p13.1) encodes a 39S protein subunit of mitochondrial ribosomes and interacts with MYC, a transcription factor required for normal facial morphogenesis. Our study illustrates not only the importance of sampling admixed populations but also the relevance of measuring the functional effects of genetic variants over gene expression to dissect the complexity of disease phenotypes.

overall_design: In order to understand the genetic basis of NSCL/P susceptibility, we searched for genetic variants with regulatory role in a disease-related tissue, the lip muscle (orbicularis oris muscle, OOM) of affected individuals. From OOM samples, which are frequently discarded during corrective surgeries that patients with orofacial clefts routinely undergo, we derived mesenchymal stem cells (OOMMSC), and correlated the individual genetic differences with gene expression. We obtained OOM samples from 43 NSCL/P-affected and four normal individuals, and established OOMMSC  primary cultures according to previously published protocol. To measure transcript levels, we used Human Gene Chip 1.0 ST v1 microarrays (Affymetrix, USA), according to the manufacturer’s protocol, using 300ng of total RNA. One patient was excluded from expression analysis.

first: C

first: L

last: Brito

first: M

middle: R

last: Passos-Bueno


title: Vaccination and topical imiquimod treatment promote immune signatures in melanoma

status: Public on Apr 01 2017

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: Infiltration of cancers by T-cells is associated with improved patient survival and response to immune therapies; however, optimal approaches to induce T-cell infiltration of tumors are not known. This study tests the hypothesis that topical treatment of melanoma metastases with the TLR7 agonist imiquimod treatment plus administration of a multipeptide cancer vaccine will improve immune cell infiltration of melanoma metastases. Patients and Methods: Eligible patients were immunized with a vaccine comprised of 12 melanoma peptides and a tetanus toxoid-derived helper peptide, and imiquimod was applied topically to tumors daily. Adverse events (AE; CTCAE v4.03) were recorded and effects on the tumor microenvironment (TME) were evaluated from sequential tumor biopsies. T-cell responses were assessed by IFNgamma ELIspot assay, and T-cell tetramer staining. Patient tumors were evaluated for immune cell infiltration, cytokine and chemokine production, and gene expression. Results and Conclusions: Four eligible patients were enrolled, and administration of imiquimod and vaccination was well tolerated in these patients. Circulating T-cell responses to the vaccine were detected by ex vivo ELIspot assay in 3 of 4 patients. Treatment of metastases with imiquimod induced immune cell infiltration and favorable gene signatures in the patients with circulating T-cell responses. This study supports further study of topical imiquimod combined with vaccines or other immune therapies for the treatment of melanoma. Precis: This clinical trial tested topical application of imiquimod to melanoma metastases combined with a melanoma vaccine. The regimen dramatically upregulated immune rejection gene signatures in melanoma metastases and increased T-cell infiltrate.

overall_design: Biopsies (incisional, core or excisional biopsies) of cutaneous or subcutaneous metastatic melanoma were obtained on day 1 (baseline, pre-treatment) (n=3), day 22 (after 3 weeks of imiquimod treatment, and 1 week after the third vaccine) (n=5) and day 43 (after 6 weeks of imiquimod, and 1 week after the 4th vaccine) (n=3).


title: Expression data from chronic myeloid leukemia and normal bone marrow stem and progenitor cells

status: Public on Apr 11 2017

city: Mexico City

first: Sócrates

last: Avilés-Vázquez

state: México City

address: Av, Cuauhtemoc 330 Col Doctores Oncology Hospital 3rd Floor

country: Mexico

institute: IMSS

summary:
Chronic myeloid leukemia is a disease originated at the level of hematopoietic stem cell, characterized by the abnormal overproduction and accumulation, both in blood and bone marrow, of myeloid cells. Treatment options include tyrosine kinase inhibitors that inhibit BCR-ABL activity, however some patients develop resistance to these drugs and has been asociated to the stem cells
We have performed a comparative analysis of the global gene expression profiles between CML and normal HSCs. Our goal was to identify key genes and pathways –preferentially, or solely, expressed by LSCs- that could be used as markers for the identification and selection of LSC LSC(CD34+ CD38- lineage-negative cells), and as targets for inhibiting the growth of such cells. We have also analyzed the population of progenitor cells (CD34+ CD38+ Lin- cells) since it has been clearly shown that these cells play an important role in the pathophysiology of CML

overall_design: Stem and progenitor cells of chronic myeloid leukemia patients and normal bone marrow were isolated by FACS, stem cells were lysed after FACS and one fraction of progenitor cells were lysed and other fraction were cultured with or without imatinib.

first: Hector

last: Mayani

first: Antonieta

last: Chávez-Gonzalez

first: Alfredo

last: Hidalgo-Miranda


title: Disrupted miRNA expression in HAND

city: Edmonton

first: William

middle: George

last: Branton

state: Alberta

address: 611 HMRC University of Alberta

institute: University of Alberta

summary:
The role of miRNA disregulation in the development of HIV associated Neurocognitive Disorder was assessed in post mortem cerebral tissue.
We used microarrays to compare the expression of miRNAs in patient with HIV showing no neurological complications to those with HAND in the presence or absence of active HIV encephalitis

overall_design: 30 post mortem human neocortex specimens were obtained from the NNTC, several of which had previously been examined using mRNA arrays, and total RNA was extracted, labelled and hybridized to Affymetrix miRNA 3.0 chips to assess specific changes in miRNA expression to provide clues to host genes with altered regulation in HAND.

first: Zaikun

last: Xu

first: Eugene

last: Asahchop

middle: G

first: Benjamin

middle: B

last: Gelman

first: Christopher

middle: N

last: Power

first: Tom

last: Hobman


title: Expression profile of human lymphatic endothelial cells in the presence or absence of TAZ

city: Lausanne

first: Nadine

last: Fournier

state: Vaud

address: Agora Cancer Research Center, Bugon 25A

country: Switzerland

institute: Agora Cancer Research Center & Swiss Institute of Bioinformatics

summary: We used microarrays to study the transcriptional networks controlled by TAZ in human lymphatic endothelial cells.

overall_design: Human lymphatic endothelial cells were seeded on plastic coated with 3µg/cm2 fibronectin, transfected with control or TAZ siRNAs. RNA were collected 48 hours post-transfection from confluent cells. RNA were amplified and hybridized on Affymetrix Human Gene 1.0 ST Arrays.  The experiment was run twice independently, using each time a different siRNA to knockdown FOXC2, as previously described (Sabine et al, 2012, Dev Cell).

first: Cansaran

last: Saygili

last: Zangger

first: Amélie

last: Sabine

first: Muriel

last: Jaquet

first: Mauro

last: Delorenzi

first: Tatiana

middle: V

last: Petrova


title: GRHL3 binding and the enhancer landscape are reorganized during transitions between different functional states of epidermal keratinocytes [siREST-proliferation]

city: Irvine

first: Bogi

last: Andersen

address: 839 Health Sciences Dr.

institute: University of California, Irvine

overall_design: pooled siRNA was used to knockdown REST in duplicate, with 2 scramble siRNA control replicates. Cells were collected 72 hours later. RNA was extracted and submitted for microarray.

first: Rachel

last: Herndon Klein


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans [AffymetrixCytoScanHD]

status: Public on Mar 23 2017

city: St. Augustine

first: Rajini

last: Haraksingh

address: The University of the West Indies

department: Life Sciences

country: Trinidad and Tobago

institute: The University of the West Indies

summary:
Background: High-resolution microarray technology is routinely used in basic research and clinical practice to efficiently detect copy number variants (CNVs) across the entire human genome. A new generation of arrays combining high probe densities with optimized designs will comprise essential tools for genome analysis in the coming years. We systematically compared the genome-wide CNV detection power of all 17 available array designs from the Affymetrix, Agilent, and Illumina platforms by hybridizing the well-characterized genome of 1000 Genomes Project subject NA12878 to all arrays, and performing data analysis using both manufacturer-recommended and platform-independent software. We benchmarked the resulting CNV call sets from each array using a gold standard set of CNVs for this genome derived from 1000 Genomes Project whole genome sequencing data. Results: The arrays tested comprise both SNP and aCGH platforms with varying designs and contain between ~0.5 to ~4.6 million probes.  Across the arrays CNV detection varied widely in number of CNV calls (4 - 489), CNV size range (~40 bp to ~8 Mbp), and percentage of non-validated CNVs (0 - 86 %). We discovered strikingly strong effects of specific array design principles on performance. For example, some SNP array designs with the largest numbers of probes and extensive exonic coverage produced a considerable number of CNV calls that could not be validated, compared to designs with probe numbers that are sometimes an order of magnitude smaller. This effect was only partially ameliorated using different analysis software and optimizing data analysis parameters. Conclusions: High-resolution microarrays will continue to be used as reliable, cost- and time-efficient tools for CNV analysis. However, different applications tolerate different limitations in CNV detection. Our study quantified how these arrays differ in total number and size range of detected CNVs as well as sensitivity, and determined how each array balances these attributes. This analysis will inform appropriate array selection for future CNV studies, and allow better assessment of the CNV-analytical power of both published and ongoing array-based genomics studies. Furthermore, our findings emphasize the importance of concurrent use of multiple analysis algorithms and independent experimental validation in array-based CNV detection studies.
NA12878 hybridization to Affymetrix CytoScan HD array for CNV detection

overall_design: We systematically compared the genome-wide CNV detection power of all 17 available array designs from the Affymetrix, Agilent, and Illumina platforms by hybridizing the well-characterized genome of 1000 Genomes Project subject NA12878 to all arrays in two technical replicates, and performing data analysis using both manufacturer-recommended and platform-independent software. We benchmarked the resulting CNV call sets from each array using a gold standard set of CNVs for this genome derived from 1000 Genomes Project whole genome sequencing data.


title: Copy number analysis of plasma cells from AL amyloidosis patients

status: Public on Mar 29 2017

city: Heidelberg

first: Martin

last: Granzow

address: INF 366

institute: University Hospital Heidelberg

summary:
Immunoglobulin light chain (AL) amyloidosis is characterized by deposition of abnormal amyloid fibrils in multiple organs impairing their function. CD138-purified plasma cells producing these fibrils are investigated regarding chromosomal alterations by interphase fluorescence in situ hybridization (iFISH) using a multiple myeloma specific probe set for the IgH translocations as well as recurrent numerical aberrations. Aberrations genuine to AL amyloidosis cannot be detected due to the inherent limitation of this probe panel to known loci. We analyzed 118 AL amyloidosis patients by high-density copy number array to quantitatively detect genome-wide chromosomal imbalances.
Most prevalent gains affected chromosomes 1q (37%), 9 (24%), 11q (24%), and 19 (16%). The most frequent deletion was monosomy 13 (28%) followed by partial deletions on 14q (21%), 16q (14%), and 13q (12%). The results were analyzed with respect to cytogenetic subgroups. In 88% of patients with translocation t(11;14) and concomitant gain of 11q22.3/11q23 detected by iFISH, the latter aberration was not due to trisomy of chromosome 11 but part of the unbalanced translocation der(14)t(11;14)(q13;q32) with breakpoint in the CCND1/MYEOV gene region. Partial loss of chromosomes 14q and 16q were significantly associated to patients with gain 1q. Our iFISH probe set is highly concordant with copy number results as it detects the most common cytogenetic aberrations present in AL amyloidosis. Beyond that, the probe panel is also the method of choice to detect translocations involving the IgH locus. In contrast to the results of our iFISH panel the frequency of hyperdiploidy detected by copy number array analysis is higher.

overall_design: Affymetrix CytoScanHD arrays were performed according to the manufacturer's directions on DNA extracted from FACS sorted CD138+ plasma cells from. 118 AL samples. Analyzed with ChAS 2.0 software using manufacturer's reference.

first: Anna

last: Jauch

first: Stefan

last: Schoenland


title: Expression data from quadriceps of utrn+/-;mdx mice treated with spironolactone plus lisinopril, eplerenone plus lisinopril or prednisolone compared to untreated

status: Public on Mar 07 2017

city: Columbus

first: Jill

last: Rafael-Fortney

state: OH

address: 460 W. 12th Ave

department: Physiology & Cell Biology

institute: The Ohio State University

summary: To identify the gene expression differences in skeletal muscles resulting from treatment of dystrophic mice with spironolactone plus lisinopril, eplerenone plus lisinopril or prednisolone.

overall_design: 12 total samples were analyzed; 3 biological replicates for each spironolactone plus lisinopril, eplerenone plus lisinopril, prednisolone, and untreated groups; a pairwise comparison between groups was carried out and a fold-change ≥2 were selected.

first: Jessica

last: Chadwick


title: Gene expression analysis of undifferentiated and differentiated human oral squamous cell carcinoma cells

city: Chiyoda-ku

first: Shogo

last: Okazaki

state: Tokyo

address: 1-8-13 Kanda-Surugadai

department: School of Dentistry

country: Japan

institute: Nihon University

summary: To analyze gene expression profiles of differentiated and undifferentiated cancer cells, oral squamous cell carcinoma cell line HSC-2 cells were cultured under normal or adhesion-restricted condition and subjected to cDNA microarray analysis.

overall_design: To induce differentiation, HSC-2 cells were seeded onto 24-well NanoCulture plate at a density of 5 × 104 cells/ml for 72 hours. Total RNAs were isolated and subjected to cDNA microarray analysis. 4 replicates were examined on each condition.

first: Kiyoko

last: Umene

first: Hideyuki

last: Saya

first: Osamu

last: Nagano


title: Comprehensive performance comparison of high-resolution array platforms for genome-wide Copy Number Variation (CNV) analysis in humans

type: Genome variation profiling by genome tiling array

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

overall_design: Refer to individual Series


title: Altered integrin expression patterns revealed by microarray in matched human melanomas (mRNA)

status: Public on Mar 01 2017

city: Budapest

first: Laura

last: Vizkeleti

address: Üllői str. 93.

department: 2nd Deptartment of Pathology

country: Hungary

institute: Semmelweis University

summary:
Metastatic process is considered the predominant cause of melanoma-specific death, decreasing survival dramatically, and resulting in difficulties in the effective treatment. Large variety of molecular pathways associated with disease development and progression suggests that no individual molecular alteration is crucial in these processes per se.
Our aim was to gain insight into the molecular alterations behind metastasis formation, and to determine to what extent the profiles of primary melanoma and the corresponding metastasis are similar or distinct. High-throughput gene expression profiling was performed in combination with DNA microarrays to define significantly altered genes between matched primary and metastatic melanoma cell lines and tissue samples. Invasive behavior of different cell lines was determined using Matrigel invasion assays, and invasive primary clones were cultured selectively. Real-time qRT-PCR was applied to define integrin expression profiles of cell line pairs and melanoma tissue samples.

overall_design: A total of 4 human melanoma cell line pairs and 2 matched fresh/frozen primary lesions and lymph node metastatses were analyzed. Melanocyte was used as reference sample for the cell lines' expression data, whereas naevus (N=8 pooled samples) and normal skin (N=5 pooled samples) were applied as reference samples for the tissue expression data.

last: Vízkeleti

first: Tímea

last: Kiss

first: Viktória

last: Koroknai

first: Szilvia

last: Ecsedi

first: Orsolya

last: Papp

first: István

last: Szász

first: Róza

last: Ádány

first: Margit

last: Balázs


title: Selectin independent adhesion during metastases of ovarian cancer

status: Public on Mar 31 2017

city: Moscow

first: Maxim

last: Shkurnikov

address: 2 bld. 85, Ugreshkaya st.

country: Russia

institute: SRC Bioclinicum

summary:
Tumor cell extravasation takes place, similar to leukocytes, in a multi-step process by which cells emigrate from the blood stream through the vascular endothelium into the tissue. Selectins are regarded as the most important molecules for the first capturing step of the cascade. Whether all tumor cells employ selectin dependent adhesion to metastasize or there is an alternative mechanism still is an open question.
Comparative transcriptomic analysis of OVCAR8 and SKOV3 cultured cells and revealed that one third of genes encoding proteins involved in the selectin dependent leukocyte like adhesion cascade show lower expression levels in OVCAR8 cultured cells in comparison to that in SKOV3 cultured cells. In contrast to SKOV3 cells, c-Fos overexpression in OVCAR8 cells does not significantly influence expression of the leukocyte like adhesion cascade genes leaving them at similar levels as in control OVCAR8 cells. The intraperitoneal xenograft model of OVCAR8 cells demonstrated that aggressiveness of OVCAR8-derived tumors is not dependent of c-Fos expression level and comparable with that for SKOV3 control tumors. Based on transcriptome array data we analyzed in details expression of genes encoding proteins involved in the leukocyte like adhesion cascade, E- and P-selectin ligands, as well as glycosylation enzymes in both type of tumors. Our results suggest that selectin-dependent mechanism is not the only for adhesion of OVCAR8 ovarian cancer cells. There is at least one additional mechanism of extravasation that does not rely on selectins.

overall_design: We studied the influence of c-Fos overexpression on transcriptomes and in vivo metastatic potential of human ovarian cancer cell line OVCAR8 in comparison of the similar earlier obtained data for SKOV3 cells. First, we performed a comparative transcriptomic analysis of OVCAR8 and SKOV3 cultured cells. Then, to find out if there is a correlation between the cascade gene expression and metastatic potential of the ovarian cancer cells with and without overexpression of c-Fos we employed the intraperitoneal xenograft model of OVCAR8 cells.

first: Nadezhda

last: Khaustova

first: Diana

last: Maltseva

first: Leticia

last: Oliveira-Ferrer

first: Christine

last: Schröder

first: Karin

last: Milde-Langosch

first: Sergey

last: Rodin

first: Julia

last: Makarova

first: Udo

last: Schumacher

first: Alexander

last: Tonevitsky


title: Affymetrix SNP array data for chronic lymphoblastic leukemia samples

status: Public on Apr 06 2017

city: Chicago

first: Carrie

last: Fitzpatrick

state: IL

address: 5841 S Maryland Ave

country: USA

institute: University of Chicago

type: Genome variation profiling by high throughput sequencing

summary: Ibrutinib (Ibr), an orally administered covalent inhibitor of Bruton’s kinase, has generated remarkable responses in CLL patients including those with an unfavorable cytogenetic profile. Once patients develop resistance to ibrutinib, the outcome is poor with few treatment options.  To further understand the genomic mechanisms underlying Ibr resistance, we’ve performed genome wide copy number analysis of serial samples collected from nine ibrutinib-relapsed patients.  Deletions of 18p often coincide with del(17p)/TP53 mutations, predispose patients to relapse.

overall_design:
Affymetrix SNP arrays were performed according to the manufacturer's directions on DNA extracted from diagnostic bone marrow, peripheral blood or lymph node samples.
Copy number analysis of Affymetrix CytoScan or OncoScan SNP arrays was performed on a total of 26 samples collected from 9 patients included in the study.
Please note that OncoScan arrays produce 2 CEL files generated from 2 separate chips that are subsequently converted and combined into one OSCHP file.

first: Sabah

last: Kadri

first: Jimmy

last: Lee

first: Natalie

last: Galanina

first: Madina

last: Sukhanova

first: Girish

last: Venkataraman

first: Shruti

last: Sharma

first: Brad

last: Long

first: Kristin

last: Petras

first: Megan

last: Theissen

first: Mei

last: Ming

first: Yuri

last: Kobzev

first: Wenjun

last: Kang

first: Ailin

last: Guo

first: Weige

last: Wang

first: Nifang

last: Niu

first: Howard

last: Weiner

first: Michael

last: Thirman

first: Wendy

last: Stock

first: Sonali

last: Smith

first: Chadi

last: Nabhan

first: Jeremy

middle: P

last: Segal

first: Pin

last: Lu

first: Y

middle: L


title: Marker chromosomes can arise from chromothripsis and predict adverse prognosis in acute myeloid leukemia

first: Martin

last: Granzow

country: Germany

summary:
Metaphase karyotyping is an established diagnostic standard in acute myeloid leukemia (AML) for risk stratification. One of the cytogenetic findings in AML are structurally highly abnormal marker chromosomes. In this study, we have assessed frequency, cytogenetic characteristics, prognostic impact and underlying biological origin of marker chromosomes. Given their inherent gross structural chromosomal damage, we speculated that they may arise from chromothripsis, a recently described phenomenon of chromosome fragmentation in a single catastrophic event. In 2 large consecutive prospective, randomized, multicenter, intensive chemotherapy trials (AML96, AML2003) from the Study Alliance Leukemia (SAL), marker chromosomes were detectable in 165/1026 (16.1%) of aberrant non-core-binding-factor (CBF) karyotype patients. Adverse-risk karyotypes displayed a higher frequency of marker chromosomes (26.5% in adverse-risk, 40.3% in complex aberrant and 41.2% in abnormality(17p) karyotypes, p<.0001 each).
Marker chromosomes were associated with a poorer prognosis compared to other non-CBF aberrant karyotypes and led to lower remission rates (CR+CRi), inferior event-free survival as well as overall survival in both trials. In multivariate analysis, marker chromosomes independently predicted poor prognosis in the AML96 trial ≤60 years. As detected by array-CGH, about one third of marker chromosomes (18/49) had arisen from chromothripsis, whereas this phenomenon was virtually undetectable in a control group of marker chromosome-negative complex aberrant karyotypes (1/34). The chromothripsis-positive cases were characterized by a particularly high degree of karyotype complexity and dismal prognosis. In conclusion, marker chromosomes are indicative of chromothripsis and associated with poor prognosis per se and not merely by association with other adverse cytogenetic features.

overall_design: Affymetrix CytoScanHD arrays were performed according to the manufacturer's directions on DNA extracted from AML samples. Analyzed with ChAS 1.0.16(r6634) software using manufacturer's reference.

first: Tilmann

last: Bochtler

first: Anna

last: Jauch


title: GDF5-induced tenogenic differentiation of human bone marrow-derived stromal cells (hMSC)

status: Public on Feb 11 2017

city: Kuala Lumpur

first: Sik Loo

last: Tan

state: Federal Territory

address: Lembah Pantai

department: Department of Orthopaedic Surgery

country: Malaysia

institute: University of Malaya

summary:
GDF5 is a potent tenogenic differentiation inducer. We previously demonstrated that GDF5 induced in vitro tenogenesis of human bone marrow-derived stromal cells (hMSC).
We used microarrays to detail the global gene expression profiles underlying tenogenesis and identified distinct classes of up-regulated genes during this process.

overall_design: hMSCs were treated with GDF5 (100 ng/ml) for 4 days and 10 days and used for total RNA extraction and hybridization on Affymetrix microarrays. hMSCs without GDF5 treatment and human tenocytes isolated from human hamstring tendon were used as a differentiated control.

first: Sik


title: Genome-wide profiling of miRNAs during differentiation of wild (WT) murine embryonic stem cells (ESCs), scrambled control (SCR) ESCs, and Strip2 silenced (KD) ESCs

status: Public on Mar 26 2017

city: Cologne

first: Agapios

last: Sachinidis

state: NRW

address: Robert-Kochstr. 39

department: Institute of Neurophysiology

institute: University of Cologne

summary:
The role of Striatin Interacting Protein 2 (Strip2) in differentiation of embryonic stem cells (ESCs) is still under debate. Strip2 silenced (KD) ESCs were differentiated for 4, 8, 12, and 16 days. We show that Strip2 is distributed in the perinucleus or nuclei of wild type (WT) undifferentiated ESCs, but is localized in high-density nuclear bodies in differentiated cells. CellNet analysis of microarray gene expression data for KD and scrambled control (SCR) embryoid bodies (EBs), as well as immunostainings of key pluripotent factors, demonstrated that KD ESCs remain undifferentiated. This occurs even in 16-day old EBs, which possessed a high tumorigenic potential. Correlated with very high expression levels of epigenetic regulator genes, Hat1 and Dnmt3, enzymatic activities of the histone acetyltransferase type B (HAT1) and DNA (cytosine-5)-methyltransferase 3 beta (DNMT3b) were higher in differentiated 16-day old KD EBs than in SCR or WT EBs. The expression levels of let-7, 290 and 302 microRNA families were opposed in KD ESCs, while KD EBs had levels comparable to WT and SCR ESCs during differentiation. This demonstrates that Strip2 is critical to the onset of differentiation, regulating expression of epigenetic regulators, HAT1 and DNMT3b, as well as microRNAs involved in pluripotency.
For a more comprehensive understanding of the potential effects of miRNA for heart development, we carried out the first study of time-resolved parallel profiling of mRNA and miRNA levels in the developing and adult (10 weeks old) as well as old (14 months old) murine heart and identify the dynamical activation or repression of numerous biological processes and signalling pathways

overall_design: Total RNA including also miRNAs from undifferentiated WT ESCs, SCR ESCs and KD ESCs as well as of 4-, 8-, 12- and 16-day EBs  was  isolated and gene expression was analysed by the Affymetrix miRNA 3.0 arrays.


title: CHCC2862_Respiratory_TimeCourse_EntryIntoPlusStationary

status: Public on Mar 15 2017

city: Cadorago

middle: Bastian

last: Pedersen

state: CO

address: Via Manzoni 29

department: R&D

institute: Sacco Srl

summary: Lactococcus lactis is the main bacterium used for food fermentation and is a candidate for probiotic development. In addition to fermentation growth, supplementation with heme in aerobic conditions activates a cytochrome oxidase, which promotes respiration metabolism. In contrast to fermentation in which cells consume energy to produce mainly lactic acid, respiration metabolism dramatically changes energy metabolism, such that massive amounts of acetic acid and acetoin are produced at the expense of lactic acid. Our goal was to investigate the metabolic changes that correlate with significantly improved growth and survival during respiration growth. Using transcriptional time course analyses, mutational analyses, and promoter reporter fusions, we uncover two main pathways that can explain the robust growth and stability of respiration cultures: The acetate pathway contributes to biomass yield in respiration, without affecting medium pH. The acetoin pathway allows cells to cope with internal acidification, which directly affects cell density and survival in stationary phase. Our results suggest that manipulation of these pathways could lead to fine tuning respiration growth, with improved yield and stability.

overall_design: Two samples are analyzed. The reference sample is at OD 2.5 (Cy3), and the two tests are at OD 5.6 and 6.4 (Cy5), respectively

first: Christel

last: Garrigues


title: Expression profiling of Sudanese visceral leishmaniasis patients pre- and post-treatment with sodium stibogluconate

status: Public on Mar 03 2017

city: North Coogee

first: Denise

last: Anderson

state: WA

address: 71 Caledonia Loop

country: Australia

institute: INSiGENe Pty Ltd

summary: Visceral leishmaniasis (VL) in Sudan caused by Leishmania donovani is fatal in susceptible individuals if untreated.  Treatment with Sodium Stibogluconate (SSG) leads to post kala azar dermal leishmaniasis (PKDL) in 58% of patients.  Here Affymetrix microarrays were used to identify genes differentially expressed in lymph nodes (N=9 paired samples) pre- and post-treatment with SSG.  Using the Bioconductor package limma, 438 genes from 28,869 post quality-control probe-sets were differentially expressed (Pnominal≤0.02) post- versus pre-treatment.  Canonical pathway analysis using Ingenuity Pathway Analysis identified “Role of NFAT in Regulation of Immune Response” (Pnominal=1.35x10-5; PBH-adjusted=4.79x10-3), “B Cell Development” (Pnominal=2.04x10-4; PBH-adjusted=0.024), “Fcγ Receptor-mediated Phagocytosis in Macrophages and Monocytes” (Pnominal=2.04x10-4; PBH-adjusted=0.024), and “OX40 Signaling” (Pnominal=2.82x10-4; PBH-adjusted=0.025) as pathways differentially regulated post- versus pre-treatment.  Major network hub genes included TP53, FN1, MYC, BCL2, JUN, SYK, RUNX2, MMP1 and ACTA2.  Top endogenous upstream regulators included IL-7 (P=2.28x10-6), TNF (P=4.26x10-6), APP (P=4.23x10-5) and SPI1/PI.1 (P=1.17x10-7).  Top predicted chemical drug regulators included the flavonoid genistein (P=4.56x10-7) and the quinoline alkaloid camptothecin (P=5.14x10-5).  These results contribute to our understanding of immuno-pathology associated with VL and response to SSG treatment.  Further replication could identify novel therapeutic strategies that improve on SSG treatment and reduce the likelihood of progression to PKDL.

overall_design: Samples were collected in Kassab Hospital, El-Gadarif State, Sudan.  Active VL cases were diagnosed by experienced clinicians on the basis of clinical signs, including fever, hepatosplenomegaly, anaemia, leukopenia, pancytopenia, and by microscopic demonstration of Leishmania amastigotes in slide films prepared from inguinal lymph node aspirates.  VL patients received the standard daily dose of 20 mg SSG per kg body weight for 30 days.  Cure was confirmed by demonstration that post-treatment lymph node aspirates were negative for parasites by microscopy.  RNA was extracted from inguinal lymph node aspirates taken from 9 paired VL patients (N=7 males, aged 7 to 19 years; N=2 females, both aged 8 years) before and after treatment (i.e. 18 samples).  Aspirate volume was equivalent to the volume of an 18Gx2.5cm fine needle.  Aspirates were directly injected into 700uL of RLT buffer (RNeasy Micro Kit; QIAGEN, UK), and RNA prepared using these kits in accordance with the manufacturer´s instruction.  RNA integrity and purity were checked using a 2100 Bioanalyzer with the RNA 6000 Nano and Pico LabChip kit (Agilent Technologies, Massy, France).  All samples had RNA integrity (RIN) values >7.


title: Gene expression changes in Mammary Luminal Progenitor cells after MEN1 silencing

status: Public on Mar 09 2017

city: Boston

first: Koen

last: Dreijerink

state: MA

address: 450 Brookline Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

summary: Female patients with multiple endocrine neoplasia type 1 are at increased risk to develop breast cancer. We analyzed gene expression after silencing of the MEN1 gene in primary human mammary luminal progenitor cells to identify menin target genes involved in mammary tumorigenesis.

overall_design: Mammary luminal progenitor cells were isolated from patient-derived normal breast tissue after tissue digestion and FACS-sorting using anitibodies directed at CD49f+ and EpCAM. After harvesting and cell sorting, cells were treated with lentiviral particles containing small hairpin RNA constructs directed against MEN1 or a control sequence and subjected to puromycin selection. Total RNA from these cells was subjected to gene expression analysis using Affymetrix Human Gene 1.0 ST Arrays. Clusters of up and down regulated genes were identified.

middle: M


title: Gene expression profile of K562 human leukemia cell line after imatinib treatement

status: Public on Mar 20 2017

city: Cincinnati

first: Mohammad

last: Azam

address: 3333 Burnet Avenue

department: Division of Experimental Hematology

institute: Cincinnati Childrens Hospital and Medical Center

summary: K562 cells when grown with erythropeitin do not respond to Imatinib. Here we are comparing the gene expression profile from imatinib resistant and sensitive cells.

overall_design: K562 cells when grown with erythropeitin do not respond to Imatinib. Here we are comparing the gene expression profile from imatinib reistant and sensitive cells.


title: CNV and expression patterns in matched human melanoma tissues and cell lines with different invasive property.

first: Laura

last: Vizkeleti

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


title: Affymetrix CytoScan® HD Array (SNP and copy number array) used on pseudarthrosis tissue from Neurofibromatosis type 1 individuals

status: Public on Feb 21 2017

city: Salt Lake City

first: Rebecca

last: Margraf

state: UT

address: 500 Chipeta Way

institute: ARUP

summary: Array data was used to confirm somatic deletion or copy neutral LOH on chromosome 17, that was inclusive of the NF1 gene.

overall_design:
Affymetrix Cytoscan arrays were performed according to the manufacturer's directions on DNA extracted from peripheral blood or from frozen pseudarthrosis tissue/bone samples.
Copy number analysis and SNP array data was performed for 3  pseudarthrosis tissue samples and one blood sample from Neurofibromatosis type 1 individuals.

first: Rong

last: Mao

first: David

middle: A

last: Stevenson


title: Gene expression analysis of normal and abnormal gingiva

status: Public on Feb 14 2017

city: Seoul

first: Seong-Oh

last: Kim

address: 250 Seongsanno, Seodaemun-gu

department: Pediatric dentistry

country: South Korea

institute: Yonsei University College of Dentistry


title: CNV 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

country: China

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: CytoScan HD arrays of matched adjacent normal, primary tumor and PVTT samples from HCC patients

first: Gu

last: Jin

first: Chen

last: Lei


title: Gene expression data from BT549 attached/suspended cells

city: Aurora

first: Jennifer

middle: K

last: Richer

department: Pathology

institute: University of Colorado Anschutz Medical Campus

summary: Cells grown in forced suspension culture mimic the early steps of metastasis.  In order to determine what might be driving the ability of TNBC cells to survive in suspension, a global gene expression profiling experiment was performed. Human triple negative breast cancer (TNBC) cell line BT549 was grown in attached or forced suspension conditions for 24 hours, then RNA was harvested to look for changes in global gene expression.

overall_design: Eight samples. Two groups in biological quadruplicate.  Group one is BT549 cells grown in normal attached conditions.  Group 2 is BT549 cells grown in forced suspension conditions.

first: Valerie

last: Barton

first: Jessica

last: Christenson

first: Michael

last: Gordon

first: Lisa

middle: I

last: Greene

first: Thomas

middle: J

last: Rogers

first: Kiel

last: Butterfield

first: Beatrice

last: Babbs

first: Nicole

last: Spoelstra

first: Nicholas

middle: C

last: D'Amato

first: Anthony

last: Elias


title: Gene expression analysis of gingival fibromatosis gingiva

summary: Gingival fibromatosis (GF) is a rare oral condition characterized by proliferative fibrous overgrowth of both the attached and marginal gingiva, and the interdental papilla. But there were no papers about gene expression of gingival fibromatosis. The aim of this study was to identify the differential expression of genes in GF using cDNA microarray analysis.

overall_design: Gingival fibromatosis gingiva tissue was collected from a GF patient. Gene expression profiles were conducted using cDNA microarray analysis.


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

status: Public on Feb 12 2017

city: Setagaya-ku

first: Mizuho

last: Sakaki

department: Maternal-Fetal Biology

institute: National Research Institute for Child Health and Development

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: Gene expression analysis of normal gingiva

first: Seong-Oh

last: Kim

summary: There were no studies about gene expression of normal gingiva before. We performed this study to compare with gene expression of gingival fibromatosis

overall_design: Normal gingival tissue was collected from nine healthy subjects. Gene expression profiles were conducted using cDNA microarray analysis.


title: Identification and characterization of kidney-enriched long intergenic non-coding RNAs

status: Public on Feb 10 2017

city: Copenhagen SV

first: Shizuka

last: Uchida

email: heart.lncrna@gmail.com, suc@dcm.aau.dk

address: Frederikskaj 10B, 2. (building C)

department: Department of Clinical Medicine

country: Denmark

institute: Aalborg University

summary: In order to provide functional data of kidney-specific long intergenic non-coding RNAs (lincRNA), loss-of-function study was conducted.

overall_design: Using HEK-293 cells, we performed microarray experiments for siRNA-mediated silencing of LOC440173 and PAXIP1-AS1.

first: Giuseppe

last: Militello


title: Escherichia coli facing ionic silver stress: correlation between the genetic, physiological and biochemical responses

status: Public on Feb 09 2017

city: Toulouse

first: Laurence

last: Girbal

address: 135 avenue de rangueil

country: France

institute: TBI

summary: The present work was devoted to a multi-level characterization of E. coli exposed to Ag+-mediated stress using for the first time an approach of integrative biology, based on the combination of physiological, biochemical and transcriptomic data sets. Bacterial growth and survival after Ag+ exposure were first quantified and related to the accumulation of intracellular silver, as detected by Nano Secondary Ion Mass Spectroscopy (NanoSIMS) at high lateral resolution. The whole transcriptomic response of E. coli cells under ionic silver-mediated stress was then characterized. Clear correlations were established between (i) cell physiology, (ii) variations in the biochemical characteristics of cell fatty acids and proteins, and (iii) regulation of gene expression. This challenging approach allowed determining key genetic markers of the E. coli response to ionic silver. In particular, we identified Ag+-mediated regulations of gene expression in correlation with growth (e.g. genes of transporters, transcriptional regulators, ribosomal proteins), necessary for ionic silver transport and detoxification (e.g. copA, cueO, mgtA, nhaR) and to cope with various stress (dnaK, pspA, metA,R, oxidoreductase genes). Regulation of gene expression after Ag+ exposure was also correlated to macromolecular modifications, such as acyl chain length (e.g. fadL, lpxA, arnA), protein secondary structure (e.g. dnaJ, htpX, degP) and cell morphology (e.g. ycfS, ycbB).

sample_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: A microarray study using total RNA recovered at 3h during separate cultures of Escherichia coli MG1655 subjected to 0, 5.0, 6.5 and 8.5 µM AgNO3. Three independent repetitions were performed for each condition of 0, 5.0, 6.5 and 8.5 µM AgNO3. Each array measures the expression level of 4,254 genes from Escherichia coli MG1655 with eight 60-mer probes per gene in duplicates.

first: Claire

last: Saulou-Bérion

first: Ignacio

last: Gonzalez

first: Brice

last: Enjalbert

first: Jean-Nicolas

last: Audinot

first: Frédéric

last: Jamme

first: Muriel

last: Cocaign-Bousquet

last: Mercier-Bonin


title: Human embryonic stem cell-derived corneal endothelial cells

city: Palo Alto

first: Jeffrey

last: Goldberg

address: 2452 Watson Ct

institute: Stanford University

summary: Aim: To generate human embryonic stem cell-derived corneal endothelial cells (hESC-CECs) for transplantation in patients with corneal endothelial dystrophies.

overall_design: 6 samples: 3 samples of human embryonic stem cell-derived corneal endothelial cells (hESC-CECs) and 3 samples of cultured adult corneal endothelial cells.

first: Kathryn

last: McCabe

first: Noelia

last: Kunzevitzky

first: Brian

last: Chiswell

first: Xin

last: Xia

first: Robert

last: Lanza


title: Gene expression analysis of MCF12A human breast cultures exposed to ethanol or acetaldehyde

city: Torrance

last: Gelfand

state: CA

address: 1124 W. Carson St

department: surgery

institute: LABiomed at Harbor UCLA,  and Charles Drew Univ

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

overall_design: Refer to individual Series


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

first: Mizuho

last: Sakaki

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: Comparison of F4/80 high and low peritoneal macrophages in H.polygyrus - Salmonella Typhimurium co-infected mice

city: Manchester

first: Dominik

middle: Andreas

last: Rückerl

address: Oxford Road

department: Faculty of Biology, Medicine and Health

country: United Kingdom

institute: The University of Manchester

summary: Macrophages are involved in many different biological processes (e.g. tissue homeostasis, embryonic development, immune defence against invading pathogens). To be able to deal with these different tasks macrophages adopt distinct activation phenotypes tailored to the situation. However, macrophages show a remarkable degree of plasticity and can change their activation phenotype in response to new environmental triggers. Macrophages recruited to the site of infection can be derived from two main sources, blood monocytes and tissue resident macrophages. Of note, different types of pathogens lead to the accumulation of different types of macrophages. Thus, we have asked here whether helminth expanded, tissue resident derived macrophages will change their activation phenotype in vivo in response to consecutive bacterial co-infection.types of macrophages.

overall_design: F4/80 high and low macrophages were isolated from the peritoneal cavity of naïve, single H.polygyrus / Salmonella Typhimurium or consecutively co-infected C57BL/6J females and sorted using flow cytometry. Four biological replicates per group were used.

last: Ruckerl

first: Leo

last: Zeef

first: Judith

middle: E

last: Allen


title: In silico characterization of miRNA and long non-coding RNA interplay in multiple myeloma (95 MM lncRNA data sets)

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

summary: The identification of deregulated microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in multiple myeloma (MM) has progressively added a further level of complexity to MM biology. In addition, the cross-regulation between lncRNAs and miRNAs has begun to emerge, and theoretical and experimental studies have demonstrated the competing endogenous RNAs (ceRNAs) activity of lncRNAs as natural miRNA decoys in pathophysiological conditions, including cancer. Currently, information concerning lncRNA and miRNA interplay in MM is virtually absent. Herein, we investigated in silico the lncRNA and miRNA relationship in a representative datasets encompassing 95 MM and 30 plasma cell leukemia patients at diagnosis and in four normal controls, whose expression profiles were generated by a custom annotation pipeline to detect specific lncRNAs. We applied target prediction analysis based on miRanda and RNA22 algorithms to 235 lncRNAs and 459 miRNAs selected with a potential pivotal role in the pathology of MM. Among pairs that showed significant correlation between lncRNA and miRNA expression levels, we identified 10 lncRNA-miRNA relationships suggestive of novel ceRNA network with relevance in MM.

overall_design: We searched for putative significant correlation between lncRNAs and miRNAs expression level in paired samples, with the support of target prediction analysis. Wilcoxon rank-sum test was applied using standard functions in R base package. The Benjamini-Hochberg method was applied for multiple testing correction. miRNA targets custom predictions were obtained for lncRNA sequences by merging the results of two different algorithms: RNA-22 version 2.0 prediction algorithm and miRanda, which both allow customizing input sequences and parameters. The RNA-22 perl script was run on the combination of the 459 miRNA and 1546 (number of different transcripts corresponding to 235 lncRNAs) lncRNA FASTA sequences selected as relevant among all the miRNAs and lncRNAs respectively detected by the arrays. Default sensitivity/specificity ratio of 1.032 was chosen, provided a minimum seed size of 7 bases with only one mismatch exception, a minimum number of 12 paired-up bases in heteroduplex with -12 Kcal/mol maximum folding energy, and no more than one G-U wobble in the seed region. The miRanda algorithm has been run under default conditions, without any a-priori restrictions on score, energy and trimming parameters.

first: Domenica

last: Ronchetti

first: Martina

last: Manzoni

first: Katia

last: Todoerti

first: Antonino

last: Neri