title: Genomic binding of PAX8-PPARG fusion protein regulates cancer-related pathways and alters the immune landscape of thyroid cancer [array]

city: Ann Arbor

institute: University of Michigan

summary: PAX8-PPARG fusion protein (PPFP) results from a t(2;3)(q13;p25) chromosomal translocation, is found in 30% of follicular thyroid carcinomas, and demonstrates oncogenic capacity in transgenic mice. A PPARG ligand, pioglitazone, is highly therapeutic in mice with PPFP thyroid carcinoma. We used our previously characterized transgenic mouse model of PPFP thyroid carcinoma to identify PPFP binding sites in vivo using ChIP-seq, and to identify genes and pathways regulated by PPFP with and without pioglitazone treatment via integration with RNA-seq and Affymetrix microarray data. This submission contains the Affymetrix microarray data. PPFP and pioglitazone regulated genes involved in lipid and fatty acid metabolism, ribosome function, immune processes, cell death and other cancer-related processes. The RNA-seq data yielded similar findings.

overall_design: Mice of genotype PPFPThy;PtenThy-/- or control genotype PtenThy-/- were treated with pioglitazone 200 parts per million in chow, or control diet, starting at 10 weeks of age for 10 weeks. Thyroid RNA was isolated and prepared for analysis on Affymetrix GeneChip mouse 430 2.0 arrays.

first: Yanxiao

last: Zhang

first: Jingcheng

last: Yu

first: Vladimir

last: Grachtchouk

first: Ronald

last: Koenig


title: ChIP-seq profiling of histone modifications and retinoid X receptor occupancy during early myogenic differentiation

status: Public on Sep 13 2017

city: Ottawa

first: Qiao

last: Li

state: Ontario

address: 451 smyth road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

type: Genome binding/occupancy profiling by high throughput sequencing

summary: While skeletal myogenesis is tightly coordinated by myogenic regulatory factors including MyoD and myogenin, chromatin modifications have emerged as vital mechanisms of myogenic regulation. We have previously established that bexarotene, a clinically approved agonist of retinoid X receptor, promotes the specification and differentiation of skeletal muscle lineage. Here, we examine a genome-wide impact of rexinoids on myogenic differentiation through integral RNA-seq and ChIP-seq analyses. We found that bexarotene promotes myoblast differentiation through the coordination of exit from the cell cycle and the activation of muscle-related genes. We uncovered a new mechanism of rexinoid action which is mediated by the nuclear receptor and largely reconciled through a direct regulation of MyoD gene expression. In addition, we determined a rexinoid-responsive residue-specific histone acetylation at a distinct chromatin state associated to MyoD and myogenin. Thus, we provide novel molecular insights into the interplay between retinoid X receptor signaling and chromatin states pertinent to myogenic programs in early myoblast differentiation.

overall_design: We explored genome-wide enrichment of H4K8ac, H3K9ac, H3K18ac, H3K27ac, H3K27me3 and RXRα signals using high throughput ChIP-seq of C2C12 myoblasts differentiated for 24 hours with or without 50 nM bexarotene (Bex or Ctl).  Proliferating myoblasts and input chromatin DNA were used as controls.


title: Small RNA-seq reveals miRNAs that may regulate pupal diapause in the flesh fly, Sarcophaga bullata

status: Public on Jun 01 2017

city: Columbus

first: Julie

middle: A

last: Reynolds

state: OH

address: 318 W 12th Ave, Aronoff Lab, rm 300

department: Evolution, Ecology, Organismal Biology

country: USA

institute: Ohio State University

type: Non-coding RNA profiling by high throughput sequencing

summary: Small RNA-seq was used to identify miRNAs in pupal stage Sarcophaga bullata and to assess differences in the abundance of miRNAs in developing and diapause (i.e. dormant) pupae.

overall_design: miRNA profiles in diapausing and nondiapausing pupae of the flesh fly, Sarcophaga bullata were discovered with RNA-seq using Illumina GAIIx. Six samples were sequenced with 3 relicate samples for nondiapause (NDH_LD) and 3 diapause (NDH_SD) replicates.

first: David

middle: L

last: Denlinger


title: The genetic landscape of mutations in Burkitt lymphoma

status: Public on Jul 01 2013

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

institute: NCSU

summary: Burkitt lymphoma is characterized by deregulation of MYC, but the contribution of other genetic mutations to the disease  is largely unknown. Here, we describe the first completely  sequenced genome from a Burkitt lymphoma tumor and  germline DNA from the same affected individual. We further  sequenced the exomes of 59 Burkitt lymphoma tumors and  compared them to sequenced exomes from 94 diffuse large  B-cell lymphoma (DLBCL) tumors. We identified 70 genes that  were recurrently mutated in Burkitt lymphomas, including  ID3, GNA13, RET, PIK3R1 and the SWI/SNF genes ARID1A  and SMARCA4. Our data implicate a number of genes in  cancer for the first time, including CCT6B, SALL3, FTCD and  PC. ID3 mutations occurred in 34% of Burkitt lymphomas and  not in DLBCLs. We show experimentally that ID3 mutations  promote cell cycle progression and proliferation. Our work  thus elucidates commonly occurring gene-coding mutations in Burkitt lymphoma and implicates ID3 as a new tumor  suppressor gene.

overall_design: Gene expression profiling on 21 Burkitt lymphomas was performed using standard Affymetrix protocols as described previously. Briefly, 1 μg of total RNA was reverse transcribed, using oligo(dT) primer to synthesize cDNA. T7 primer was used for in vitro transcription, resulting in labeled cRNA, which was fragmented and hybridized to Affymetrix Whole-Genome Gene 1.0 ST microarrays. Microarrays were washed and scanned, and the data were normalized as described previously.

first: Cassandra

last: Love

first: Zhen

last: Sun

first: Guojie

first: Jenny

first: Rodney

last: Miles

first: Kristy

last: Richards

first: Cherie

middle: H

last: Dunphy

first: William

middle: W

last: Choi

first: Gopesh

last: Srivastava

first: Patricia

last: Lugar

last: Rizzieri

first: Anand

middle: S

last: Lagoo

first: Leon

last: Bernal-Mizrachi

first: Karen

middle: P

last: Mann

first: Christopher

middle: R

last: Flowers

first: Kikkeri

middle: N

last: Naresh

first: Andrew

middle: M

last: Evens

first: Amy

last: Chadburn

first: Leo

middle: I

last: Gordon

first: Magdalena

middle: B

last: Czader

first: Javed

last: Gill

first: Eric

middle: D

last: Hsi

first: Adrienne

last: Greenough

first: Andrea

last: Moffitt

first: Matthew

last: McKinney

first: Anjishnu

last: Banerjee

last: Grubor

first: Shawn

last: Levy

last: Dunson

first: Sandeep

last: Dave


title: ATF4 Licenses C/EBPb Activity in Human Mesenchymal Stem Cells Primed for Adipogenesis

status: Public on Jun 25 2015

city: Philadelphia

first: David

middle: J

last: Steger

state: PA

address: 12-193 SCTR 3400 Civic Center Blvd

department: Institute of Diabetes, Obesity, and Metabolism

institute: University of Pennsylvania

summary: We report ChIP-seq for C/EBPb and ATF4 in human mesenchymal stem cells and in a cell-free system using naked genomic DNA. ChIP-Seq for GR, RNA Polymerase II, and H3K27 acetylation in hMSCs cultured under different adipogenic conditions are also presented.

overall_design: hMSCs cultured at high or low cell seeding densities in the presence or absence of adipogenic induction cocktail

first: Daniel

last: Cohen


title: Iron stimulon and Fur regulon

status: Public on Aug 15 2013

city: Sao Paulo

first: Rogerio

last: Lourenco

state: Sao Paulo

address: Av. Prof. Lineu Prestes, 748

department: Bioquimica

country: Brazil

institute: Universidade de Sao Paulo

summary: In the alpha subclass of proteobacteria iron homeostasis is controlled by diverse iron responsive regulators. Caulobacter crescentus, an important freshwater α-proteobacterium, uses the ferric uptake repressor (Fur) for such purpose. However, the impact of the iron availability on the C. crescentus transcriptome and an overall perspective of the regulatory networks involved remain unknown. In this work we report the identification of iron-responsive and Fur-regulated genes in C. crescentus using microarray-based global transcriptional analyses. We identify 46 genes that were strongly upregulated both by mutation of fur and by iron limitation condition. Among them, there are genes involved in iron uptake (four TonB dependent receptor gene clusters, feoAB), riboflavin biosynthesis and some genes encoding hypothetical proteins. Most of these genes are associated with Fur binding sites, implicating them as direct targets of Fur-mediated repression. These data were validated by β-galactosidase and EMSA assays for two operons encoding putative transporters. The role of Fur as a positive regulator is also evident, given that 50 genes were downregulated both by mutation of fur and under low-iron condition. As expected, this group includes many genes involved in energy metabolism, mostly iron-using enzymes. Surprisingly, are also included in this group many genes encoding TonB dependent receptors and the genes fixK, fixT and ftrB encoding an oxygen signaling network required for growth during hypoxia. Bioinformatics analyses performed in the promoters of these genes suggest that positive regulation by Fur is mainly indirect. In addition to the Fur modulon, iron limitation altered expression of more 103 genes, including upregulation of genes involved in Fe-S cluster assembly, oxidative stress and heat shock response, as well as downregulation of genes implicated in amino acid metabolism, chemotaxis and motility. Altogether, our results showed that adaptation of C. crescentus to iron limitation involves increasing the transcription of iron-acquisition systems and decreasing the production of iron-using proteins as a general strategy

overall_design: Two experimental procedures, each of them performed in two replicates. A total of four independent biological samples were used

first: José

middle: F

last: da Silva Neto

first: Rogério

last: Lourenço

first: Marilis

middle: V

last: Marques


title: Gene expression profile of the germaniumu dioxide-related hearing loss cochlea in CBA mice

status: Public on Jul 22 2016

city: Bunkyo-ku

first: AKINORI

last: KASHIO

state: Tokyo

address: 7-3-1 Hongo

department: Otolaryngology

country: Japan

institute: The University of Tokyo

summary: Various organ failure induced by chronic intake of GeO2 is one of the well known disease related to mitochondrial dysfunction. The 0.15% GeO2 treated CBA mice shows severe hearing loss in 4M. Here we analyzed cochlear gene expression of 6 months old CBA mice using microarrays treated with normal chow or that containing 0.15% GeO2 for four months. Auditory brainstem response (ABR) analysis confirmed that severe age-related hearing loss occured in GeO2 treated mice, whereas no hearing loss occured in normal chow treated mice. Comprehensive gene expression analysis identified genes correlated with GeO2-induced mithochodrial dysfunction genes and revealed that  28 genes encoding components of the mitochondrial respiratory chain were significantly down-regulated. These observations provide evidence that GeO2-induced hearing loss is associated with the down-regulation of genes involved in the mitochondrial respiratory chain complexes in the cochlea of CBA mice.

overall_design: To determine the effects of GeO2, each control sample (n=5) was compared to each GeO2-intoxicated (n=5), generating a total of 25 pairwise comparisons. Using DAVIS and EASE, the identified genes were assign to “GO: Biological Process” categories of Gene Ontology Consortium. Furthermore, we used EASE to determine the total number of genes that were assigned to each biological process category, and to perform Fisher exact test. Quality control measures were not used. No replicates were done. Dye swap was not used.

first: A

last: Kashio

first: S

last: Someya


title: Genomic binding and regulation of gene expression by the thyroid carcinoma-associated PAX8-PPARG fusion protein

status: Public on Jan 21 2016

first: Maureen

last: Sartor

state: MI

address: 2017 Palmer Commons Bldg., 100 Washtenaw Ave

department: Department of Computational Medicine and Bioinformatics

type: Expression profiling by high throughput sequencing

summary: A chromosomal translocation results in production of an oncogenic PAX8-PPARG fusion protein (PPFP) in a subset of thyroid carcinomas. PAX8 is an important thyroid transcription factor, and PPARG is a transcription factor that plays important roles in the biology of adipocytes and macrophages, but has no known function in the thyroid. PPFP retains the DNA binding domains of both proteins. However, the genomic DNA binding sites of PPFP have not been identified, and only limited data exist to characterize gene expression in PPFP thyroid carcinomas. Therefore, we expressed PPFP in PCCL3 rat thyroid cells and used ChIP-seq to identify PPFP genomic binding sites (PPFP peaks) and RNA-seq to characterize PPFP-dependent gene expression. The genome contains ~20 000 PPFP peaks, including known PAX8 and PPARG binding sites, indicating that both DNA binding domains are functional. PPFP binds to and regulates many genes involved in cancer-related processes such as development and cell division. PPFP also binds to and regulates many genes related to mitochondria and lipid metabolism that are regulated by PPARG in adipocytes. Our data highlight the complexity of PPFP as a transcription factor and the numerous ways that it regulates thyroid oncogenesis.

overall_design: The rat PCCL3 thyroid cell line was stably transfected with human PAX8-PPARG fusion protein (PPFP, myc-tagged) or empty vector. For RNA-Seq, cells were cultured  ±1 μM pioglitazone for 16 hours before RNA isolation, and 3 independent experiments were performed. For ChIP-seq, cells were cultured  with 1 μM pioglitazone for 16 hours and IP was performed with anti-myc tag antibody.

first: Ronald

last: Koenig

first: Yanxiao

last: Zhang

first: Chee

last: Lee

first: Jingcheng

last: Yu

first: Bin

last: Xu


title: Genetic Heterogeneity of DLBCL

status: Public on Jan 23 2013

first: Dereje

last: Jima

summary: Diffuse large B-cell lymphoma (DLBCL) is the most common form of lymphoma in adults. The disease exhibits a striking heterogeneity in gene expression profiles and clinical outcomes, but its genetic causes remain to be fully defined. Through whole genome and exome sequencing, we characterized the genetic diversity of DLBCL. In all, we sequenced 73 DLBCL primary tumors (34 with matched normal DNA). Separately, we sequenced the exomes of 21 DLBCL cell lines. We identified 322 DLBCL cancer genes that were recurrently mutated in primary DLBCLs. We identified recurrent mutations implicating a number of known and not previously identified genes and pathways in DLBCL including those related to chromatin modification (ARID1A and MEF2B), NF-κB (CARD11 and TNFAIP3), PI3 kinase (PIK3CD, PIK3R1, and MTOR), B-cell lineage (IRF8, POU2F2, and GNA13), and WNT signaling (WIF1). We also experimentally validated a mutation in PIK3CD, a gene not previously implicated in lymphomas. The patterns of mutation demonstrated a classic long tail distribution with substantial variation of mutated genes from patient to patient and also between published studies. Thus, our study reveals the tremendous genetic heterogeneity that underlies lymphomas and highlights the need for personalized medicine approaches to treating these patients.

overall_design: 21 DLBCL cell lines and 70 DLBCL patient samples.

first: Zhang

last: Jenny

first: Grubor

last: Vladimir

first: Jima

last: Dereje

first: Dave

last: Sandeep


title: The Epstein-Barr virus induced tumor suppressor miR-34a is growth promoting in EBV-infected B cells

status: Public on Apr 20 2012

summary: Epstein-Barr virus (EBV) infection of primary human B cells drives their indefinite  proliferation into lymphoblastoid cell lines (LCLs). B cell immortalization depends on expression of viral latency genes as well as the regulation of host genes. Given the important role of miRNAs in regulating fundamental cellular processes, in this study we assayed changes in host miRNA expression during primary B cell infection by EBV. We observed and validated dynamic changes in several miRNAs from early proliferation through immortalization; oncogenic miRNAs were induced and tumor suppressor miRNAs were largely repressed. However, one miRNA described as a p53-targeted tumor suppressor, miR-34a, was strongly induced by EBV infection and expressed in many EBV and KSHV-infected lymphoma cell lines. The EBV latent membrane protein 1 (LMP1) was sufficient to induce miR-34a requiring downstream NFκB activation, but independent of functional p53. Furthermore, over-expression of miR-34a was not toxic in several B lymphoma cell lines and inhibition of miR-34a impaired the growth of EBV transformed cells. This study identifies a pro-growth role for a tumor suppressive miRNA in oncogenic virus-mediated transformation highlighting the importance of studying miRNA function in different cellular contexts.

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus
Human alphaherpesvirus 1
Human betaherpesvirus 5
Murid betaherpesvirus 1
human gammaherpesvirus 4
JC polyomavirus
Human immunodeficiency virus 1
Murid gammaherpesvirus 4
Human gammaherpesvirus 8
Betapolyomavirus hominis
Betapolyomavirus macacae

overall_design: miRNA expression profiling of human B-cells, EBV-infected, proliferating B cells and Monoclonal LCLs from 3 different donors was conducted with the use of up to 2 μg total RNA for sample

first: Eleonora

last: Forte

first: Raul

last: Salinas

first: Christina

last: Chang

first: Ting

last: Zhou

first: Sarah

last: Linnstaedt

first: Eva

last: Gottwein

first: Cassandra

last: Jacobs

first: Qi-Jing

last: Li

first: Sandeep

last: Dave

first: Micah

last: Luftig


title: To identify alterations induced in gastric mucosa of mice exposed to Pteridium aquilinum and/or infected with Helicobacter pylori

status: Public on Sep 08 2011

city: La Jolla

first: Steven

last: Head

state: CA

address: 10550 N Torrey Pines Rd

institute: The Scripps Research Institute

summary: The aim of this study is to identify alterations induced in gastric mucosa of mice exposed to Pteridium aquilinum and/or infected with Helicobacter pylori, in order to identify genes that are induced by bracken fern exerts exacerbating effects on gastric lesions associated to the infection.

overall_design:
Six groups of C57Bl/6 mice were be used:  1) control, 2) infected Helicobacter pylori, 3) treated with Bracken fern extract orogastrically, 4) treated with Bracken fern extract in drinking water, 5) infected Helicobacter pylori + treated with Bracken fern extract orogastrically, 6) infected Helicobacter pylori + treated with Bracken fern extract in drinking water. The infection procedure was performed using an orogastric inoculation of H.pylori (strain SS1) twice in the first week.  The RNA isolation was done in triplicate (3 mice per each condition).
Further evaluation of morphological alterations on gastric mucosa, proliferative index and induction of DNA strand breaks will be performed in the mice stomach exposed to Pteridium aquilinum infected or not with Helicobacter pylori. Alterations of glycosylation in gastric tissues will also evaluated.

first: Celso

last: Reis

first: Alex

middle: T

last: Moffit


title: Deep Sequencing of the Small RNA Transcriptome of Normal and Malignant Human B cells Identifies Hundreds of Novel MicroRNAs: microarray analysis

status: Public on Aug 26 2010

first: Dereje

last: Jima

summary:
A role for microRNAs has been recognized in nearly every biological system examined thus far. A complete delineation of their role must be preceded by the identification of all microRNAs present in any system. We elucidated the complete small RNA transcriptome of normal and malignant B cells through deep sequencing of 31 normal and malignant human B cell samples that comprise the spectrum of B cell differentiation and common malignant phenotypes. We identified the expression of 333 known microRNAs, which is over twice the number previously recognized in any tissue type. We further identified the expression of 286 candidate novel microRNAs in normal and malignant B cells. These microRNAs were validated at a high rate (92%) using quantitative PCR and we demonstrated their application in the distinction of clinically relevant subgroups of lymphoma.
Here, we analyzed the expression of 100 diffuse large B-cell lymphoma (DLBCL) samples using microarrays.

overall_design: Total RNA was extracted from frozen patient samples.  The RNA was labeled, fragmented and hybridized to Human Gene 1.0 ST arrays.


title: Massively Parallel Sequencing Identifies the MicroRNA Transcriptome of Normal and Malignant Human B cells

summary: Profiling of miRNA transcriptome in Human mature B cells from similar populations

overall_design: Profiling of miRNA transcriptome in Human Normal and Malignant B cells, 8 normal samples corresponding to Naïve, Germinal Center, Plasma  and Memory B cells and 23 samples derived from B cell malignancy

first: Jenny

last: Zhang


title: Genomic binding of PAX8-PPARG fusion protein regulates cancer-related pathways and alters the immune landscape of thyroid cancer [seq]

status: Public on Dec 21 2016

first: Maureen

last: Sartor

summary: PAX8-PPARG fusion protein (PPFP) results from a t(2;3)(q13;p25) chromosomal translocation, is found in 30% of follicular thyroid carcinomas, and demonstrates oncogenic capacity in transgenic mice. A PPARG ligand, pioglitazone, is highly therapeutic in mice with PPFP thyroid cancer. However, only limited data exist to characterize the binding sites and oncogenic function of PPFP, or to explain the observed therapeutic effect of pioglitazone. Here we used our previously characterized transgenic mouse model of PPFP follicular thyroid carcinoma to identify PPFP binding sites in vivo using ChIP-seq, and to distinguish genes and pathways regulated directly or indirectly by PPFP with and without pioglitazone treatment via integration with RNA-seq data. PPFP bound to DNA regions containing the PAX8 and/or the PPARG motif, near genes involved in lipid metabolism, the cell cycle, apoptosis, and cell motility; the binding site distribution was highly concordant with our previous study in a rat PCCL3 cell line. Most strikingly, pioglitazone induced an immune cell infiltration including macrophages and T cells only in the presence of PPFP, which may be central to its therapeutic effect.

overall_design: Mice of genotype PPFPThy;PtenThy-/- or control genotype PtenThy-/- were treated with pioglitazone 200 parts per million in chow, or control diet, starting at 10 weeks of age for 10 weeks. Thyroid RNA was isolated and prepared for RNA-seq analysis and microarray (included in GSE85583). ChIP-seq of PPFP was also performed twice on mice of genotype PPFPThy;PtenThy-/- treated with pioglitazone.

first: Yanxiao

first: Jingcheng

last: Yu

first: Vladimir

last: Grachtchouk

first: Ronald

last: Koenig


title: B cell subsets from human tonsil and blood

status: Public on Sep 19 2008

summary: B cells from human tonsil and blood were sorted using flow cytometry. The human samples were processed immediately ex-vivo using markers for known B cell subsets.

overall_design: Human B cell subsets from tonsil and blood investigated for analysis with gene expression

first: Patricia

last: Lugar


title: Transcriptional profiling of rag1 deficient (rag1-/-) and rag1 heterozygous (rag1+/-) zebrafish kidney and intestine

status: Public on Jan 05 2009

summary:
Four dual hybridizations of rag1 deficient (rag1-/-) and rag1 heterozygous (rag1+/-) zebrafish cRNAs from kidney and intestine.

Keywords: Gene knockout

overall_design: Four dual hybridizations: 1) Cy3-rag1+/- kidney cRNA and Cy5-rag1-/- kidney cRNA, 2) Cy5-rag1+/- kidney cRNA and Cy3-rag1-/- kidney cRNA, 3) Cy3-rag1+/- intestine cRNA and Cy5-rag1-/- intestine cRNA, and 4) Cy5-rag1+/- intestine cRNA and Cy3-rag1-/- intestine cRNA.

first: Jeffrey

last: Yoder


title: Deep Sequencing of the Small RNA Transcriptome of Normal and Malignant Human B cells Identifies Hundreds of Novel MicroRNAs

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

overall_design: Refer to individual Series


title: B cell subsets

status: Public on Aug 07 2008

summary:
Sorted B cells using flow cytometry
CD19 selected B cells were sorted using flow cytometry

overall_design: 3 replicates of 4 B cell types


title: Trascriptional profiling of angiogenic inhibitors

status: Public on Dec 31 2005

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

country: Italy

institute: University of Padova

summary:
To examine angiogenesis inhibitor-regulated pathways, the alteration in gene expression of human microvascular endothelial cells after a 4-hour treatment with seven chemically different inhibitors has been analyzed. Specifically, this series describes the expression profiles following treatment with either:
1. recombinant interferon-alpha (IFN-alpha);
2. pigment epithelium derived factor (PEDF);
3. all trans-retinoic acid (RA);
4. thrombospondin 1 (TSP-1);
5. TNP-470 (TNP-470);
6. endostatin (ENDO);
7. angiostatin (ANGIO).
To ensure that cDNA products were proportional to the initial gene expression pattern, 33P-labelled probes from oligo d(T) primed reverse transcription of 5 microg RNA were generated for each. This, followed by second strand synthesis, was used to hybridize the nylon filters (GF211 ) comprising a total of 4132 genes and EST’s.
Keywords = Homo sapiens
Keywords = human micro vascular endothelial cell
Keywords = angiogenesis
Keywords = angiogenic inhibitors
Keywords: other

first: Edith

last: Cline

first: Carlo

last: Di Bello

first: Mark

last: Lingen


title: heart gene expression in Down syndrome

status: Public on Nov 21 2004

city: Napoli

first: Lucio

last: Nitsch

address: Via Pansini 5

department: Biologia e Patologia Cellulare e Molecolare

institute: Unversity of Naples Federico II

summary:
Expression profiles in normal and Down syndrome fetal heart explants.
Keywords: other


title: B-ALL relapse analysis

status: Public on Jun 13 2003

summary:
A comparison of RNA expression profiles from leukemic cells of 8 single B-ALL patients at diagnosis and relapse. For all patients, clonality of the blast cells at diagnosis and relapse was demonstrated to be the same (Germano, G., del Giudice, L., Palatron, S., Giarin, E., Cazzaniga, G., Biondi, A., Basso, G., Clonality profile in relapsed precursor-B-ALL children by GeneScan and sequencing analyses. Consequences on minimal residual disease monitoring. Leukemia, 2003).
The study protocol was approved by the Research committee of the AIEOP and written informed consent was obtained from all participants before samples were taken. RNA extracted from BM samples was used for microarray analysis. The blast cell infiltration both at diagnosis and relapse was 75% and mononuclear cell were isolated using a Lymphoprep density gradient (1.077 g/ml, Nycomed Pharma, Oslo, Norway).
RNA was extracted from blast cells at diagnosis and relapse and both samples were hybridized on an MWG 30K Human Array A (MWG, München) after direct labeling using two different fluorochromes (Cy3 and Cy5) for the respective samples.
Keywords = Homo sapiens, B-lymphoblastic leukemia, diagnosis, relapse

first: Andrea

last: Rinaldi

first: Geertruy

last: te Kronnie

first: Liza

last: Franceschini

first: Giuseppe

last: Basso


title: Patterns of micro RNA expression characterize stages of human B-cell differentiation

status: Public on Mar 17 2009

first: Dereje

last: Jima

summary: Mature B-cell differentiation provides an important mechanism for the acquisition of adaptive immunity. Malignancies derived from mature B-cells constitute the majority of leukemias and lymphomas. These malignancies often maintain the characteristics of the normal B-cells that they are derived from, a feature that is frequently used in their diagnosis. The role of microRNAs in mature B-cells is largely unknown. Through concomitant microRNA and mRNA-profiling, we demonstrate a potential regulatory role for microRNAs at every stage of the mature B-cell differentiation process. Further, we have experimentally identified a direct role for the microRNA-regulation of key transcription factors in B-cell differentiation: LMO2 and PRDM1 (Blimp1). We also profiled microRNA of B-cell tumors derived from diffuse large B cell lymphoma, Burkitt lymphoma and chronic lymphocytic leukemia. We found that in contrast to many other malignancies, common B-cell malignancies do not down-regulate microRNAs, but rather maintain the microRNA-expression patterns of their normal B-cell counterparts. Further, each tumor-type maintained the expression of the lineage-specific microRNAs and expression of these lineage-specific microRNAs could correctly predict the lineage of B-cell malignancies in over 90% of the cases. Thus, our data demonstrate that microRNAs may be important in maintaining the mature B-cell phenotype in normal and malignant B-cells.

overall_design: Burkitt lymphoma, Chronic Lymphocytic Leukemia (Mutated), Chronic Lymphocytic Leukemia (Unmutated), Activated B cell-like Diffuse large B cell lymphoma, and Germinal Center-like Diffuse large B cell lymphoma Samples,

first: Cassandra

last: Jacobs

first: Sandeep

last: Dave


title: Overlap in Signaling through Smoothened and the Heterotrimeric G Protein G13

status: Public on May 05 2018

first: David

last: Manning

address: 3620 Hamilton Walk

summary: RNA sequencing is used to compare genes regulated by a constitutively active form of Smoothened, a protein critical to Hedgehog signaling, and a constitutively active form of the alpha subunit of the heterotrimeric G proteins G13, which shares some of the primary actions of Smoothened.

overall_design: Constitutively active forms of Smoothened and the alpha subunit of G13, and as a control LacZ, were introduced into C3H10T/12 cells by means of recombinant adenoviruses. RNA was isolated 48 h thereafter for sequencing.

first: Xueshui

last: Guo

first: Natalia

last: Riobo-Del Galdo

first: Eun

last: Kim

first: Gregory

last: Grant