title: Interferon receptor signaling pathways regulating PD-L1 and PD-L2 expression

status: Public on May 09 2017

first: Willy

last: Hugo

summary: We studied the molecules involved in downstream signaling induced by interferons to regulate PD- L1 and PD-L2 expression using a shRNA screen, Western blot, mRNAexpression profiling, promoter truncation analysis and chromatin immunoprecipitation.These studies revealed that the interferon gamma-JAK1/2-STAT1-IRF1 axis primarily regulates PD-L1 expression, with IRF1 binding to its promoter. PD-L2 responded equally to interferon beta and gamma, and shared regulation through IRF1 and alsoSTAT3, which bind to the PD-L2 promoter. Analysis of biopsies from patients with melanoma confirmed interferon signature enrichment and upregulation of gene targets for STAT1/2/3 and IRF1 in anti-PD-1 responding tumors. Therefore, these studies map the signaling pathway of interferon-inducible PD-1 ligand expression

overall_design: Melanoma biopsies pre and on- anti-PD-1 treatment were sent for transcriptomic analysis by paired end RNAseq analysis

first: Angel

last: Garcia-Diaz

first: Daniel

last: Shin

first: Blanca

last: Moreno

first: Justin

last: Saco

first: Helena

last: Escuin-Ordinas

first: Gabriel

last: Rodriguez

first: Jesse

last: Zaretsky

last: Sun

first: Xiaoyan

last: Wang

first: Giulia

last: Parisi

first: Cristina

last: Saus

first: Davis

middle: Y

last: Torrejon

first: Thomas

last: Graeber

first: Begonya

first: Siwen

last: Hu-Lieskovan

first: Robert

last: Damoiseaux

first: Roger

last: Lo

first: Antoni

last: Ribas


title: Nutritional and Pharmaceutical Interventions in Diabetic Rats

status: Public on Feb 08 2017

city: Guelph

first: David

middle: M

last: Mutch

state: Ontario

address: 50 Stone Road East

department: Human Health & Nutritional Sciences

country: Canada

institute: University of Guelph

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

overall_design: Refer to individual Series


title: Loss of Asxl1 Alters Mesenchymal Stem Cell Fate through H3K4me3

status: Public on Jul 01 2016

city: Tianjin

first: Caiying

last: Zhu

address: Heping District, Nanjing Road, 288

country: China

institute: Institute of Hematology and Blood Disease Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing


title: RNA-Seq Analysis of Dose-Dependent TCDD-Elicited Duodenal Gene Expression in Male Mice

status: Public on Feb 28 2017

city: East Lansing

first: Timothy

last: Zacharewski

state: Michigan

address: 603 Wilson Road

department: BMB

country: USA

institute: Michigan State University

summary: Dose-dependent duodenal gene expression was examined following repeated exposure (every 4 days for 28 days) to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). These data were used to examine the effect of repeated TCDD exposure on gene expression in the intestinal epithelium of C57BL/6 male mice.

overall_design: Three biological replicates for each dose (0.01, 0.03, 0.1, 0.3, 1, 3, 10, 30) of TCDD and sesame oil vehicle

first: Kelly

middle: A

last: Fader

first: Rance

last: Nault

middle: R


title: Loss of Asxl1 Alters Self-Renewal and Cell Fate of Bone Marrow Stromal Cell

status: Public on Jun 30 2016

summary: De novo ASXL1 mutations are found in patients with Bohring-Opitz syndrome, a disease with severe developmental defects and early childhood fatality. The underlying pathologic mechanisms remain largely unknown. Using Asxl1-targeted murine models,we found that Asxl1 global loss or conditional deletion in osteoblasts and their progenitors in mice leads to significant bone loss and markedly decreased numbers of marrow mesenchymal stem/progenitor cells (MSPCs) compared with wild-type (WT) littermates. Asxl1-/- MSPCs displayed impaired self-renewal and skewed differentiation-away from osteoblasts and favoring adipocytes. RNA-seq analysis reveals the altered expression of genes involved in cell proliferation, skeletal development and morphogenesis. Furthermore, gene set enrichment analysis showed a decreased gene expression of stem cell self-renewal signature,suggesting the role of Asxl1 in regulating the stemness of MSPCs. Importantly, introducing Asxl1 normalized NANOG and OCT4 expression and restored the self-renewal capacity of Asxl1-/- MSPCs. Our study unveils a pivotal role of ASXL1 in maintenance of MSPC functions and skeletal development.

overall_design: Examination of mRNA profiles in wild type and Asxl1-/- MSPCs by deep sequencing

first: Peng

last: Zhang

first: Caihong

last: Xing

first: Qian

middle: F

first: Feng

middle: C

last: Yang


title: Gene expression profiles in rat lung following intratracheal instillation with short size single-wall and multi-wall carbon nanotubes

status: Public on Nov 19 2015

city: Tsukuba

first: Katsuhide

last: Fujita

address: 16-1 Onogawa

department: Research Institute of Science for Safety and Sustainability

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

summary: To further development of our gene expression approach to assess the effects of manufactured nanomaterials at the transcriptional level, we have employed whole genome microarray expression profiling to discuss the differences of the pulmonary and pleural

overall_design: Groups of nine-week-old male Wistar rats (n = 4 per group/ time point) were intratracheally instilled with short SWCNTs and MWCNTs suspended in 0.4 mL of 10mg/mL bovine serum albumin (BSA) as a single injection, respectively. Control groups received 10mg/

first: Makiko

last: Fukuda


title: mRNA expressions in pre-treatment melanomas undergoing anti-PD-1 checkpoint inhibition therapy

status: Public on Mar 18 2016

city: Los Angeles

first: Willy

last: Hugo

state: California

address: 10833 Le Conte Ave

department: Medicine

institute: University of California, Los Angeles

summary: PD-1 immune checkpoint blockade provides significant clinical benefits for cancer patients. However, factors influencing innate sensitivity remain incompletely catalogued. We analyzed the somatic mutanomes and transcriptomes of pretreatment melanoma biopsies. Mutations in cell adhesion genes and the DNA repair gene BRCA2 were enriched in responding tumors, and a high mutational load associated with improved survival. Innately resistant tumors displayed frequent transcriptomic up-expression of genes that enriched for mesenchymal transition, cell adhesion, ECM organization, wound-healing and angiogenesis. The transcriptomes of innate resistance also enriched for signatures indicating up-regulation of these processes. Notably, MAPK-targeted therapy (MAPKi) induced similar signatures in melanoma, suggesting that a form of MAPKi resistance mediates cross-resistance to anti-PD-1 therapy. Co-enrichment of IPRIM (Innate anti-PD-1 Resistance Induced by MAPKi) signatures defined a transcriptomic subset across advanced cancers, suggesting that attenuating processes underlying these signatures may augment anti-PD1 responses. Thus, multi-factorial determinants influence anti-PD-1 patterns in melanoma.

overall_design: Melanoma biopsies pre-anti-PD-1 therapy were sent for transcriptomic analysis by paired-end RNAseq analysis to find the correlates of response vs. non-response to the therapy

first: Jesse

last: Zaretsky

first: Lu

last: Sun

first: Chunying

last: Song

first: Blanca

last: Homet-Moreno

first: Beata

last: Berent-Maoz

first: Jia

last: Pang

first: Bartosz

last: Chmielowski

first: Grace

last: Cherry

first: Elizabeth

last: Seja

first: Shirley

last: Lomeli

first: Xiangju

last: Kong

first: Mark

last: Kelley

first: Jeffrey

last: Sosman

first: Douglas

middle: B

last: Johnson

middle: S


title: SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers [array]

status: Public on Aug 01 2015

city: Cincinnati

first: Matthew

last: Weirauch

state: Ohio

address: 3333 Burnet Avenue

department: Center for Autoimmune Genomics and Etiology (CAGE)

institute: Cincinnati Children's Hospital Medical Center

type: Genome binding/occupancy profiling by array

summary: Development of an alternative method to ChIP for the identification of DNA bound by transcriptional complexes assayed using Nimblegen arrays

overall_design: Nimblegen promoter arrays allowing identification of sites bound by different Notch complexes using SpDamID

first: Raphael

last: Kopan

last: Hass


title: Methylation changes in pre MAPKi treatment and post MAPKi resistance Melanomas

status: Public on Sep 15 2015

first: Willy

last: Hugo

type: Methylation profiling by genome tiling array

summary: Melanoma resistance to MAPK- or T cell checkpoint-targeted therapies represents a major clinical challenge, and treatment failures of MAPK-targeted therapies due to acquired resistance often require salvage immunotherapies. We show that genomic analysis of acquired resistance to MAPK inhibitors revealed key driver genes but failedto adequately account for clinical resistance. From a large-scale comparative analysis of temporal transcriptomes from patient-matched tumor biopsies, we discovered highly recurrent differential expression and signature outputs of c-MET, LEF1 and YAP1 as drivers of acquired MAPK inhibitor resistance. Moreover, integration of gene- and signature-based transcriptomic analysis revealed profound CD8 T cell deficiency detected in half of resistant melanomas in association with downregulation of dendritic cells and antigen presentation. We also propose a major methylomic basis to transcriptomic evolution under MAPK inhibitor selection. Thus, this database provides a rich informational resource, and the current landscape represents a benchmark to understanding melanoma therapeutic resistance.

overall_design: Melanoma biopsies pre and post MAPKi treatment were sent for DNA methylation analysis using Illumina Human Methylation 450K bead chips

first: Hubing

last: Shi

first: Marco

last: Piva

first: Gatien

last: Moriceau

first: Aayoung

last: Hong

first: Kimberly

last: Dahlman

first: Antoni

last: Ribas

first: Roger

last: Lo


title: Expression changes in pre MAPKi treatment and post MAPKi resistance Melanomas

overall_design: Melanoma biopsies pre and post MAPKi treatment were sent for transcriptomic analysis using Affymetrix HuGene 2.1 microarray

first: Lu

last: Sun

first: Chunying

last: Song


title: SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers


title: RNAseq changes in pre MAPKi treatment and post MAPKi resistance Melanomas

overall_design: Melanoma biopsies pre and post MAPKi treatment were sent for RNAseq analysis

last: Kong


title: SpDamID: Marking DNA Bound by Protein Complexes Identifies Notch-Dimer Responsive Enhancers [next-generation sequencing]

summary: Development of an alternative method to ChIP for the identification of DNA bound by transcriptional complexes assayed using next-generation sequencing

overall_design: Next-generation sequencing data from sites identified by different Notch complexes using SpDamID-seq and compared against FAIRE and ChIP data


title: Aspp1 Preserves Hematopoietic Stem Cell Pool Integrity and Prevents Malignant Transformation

status: Public on May 20 2015

city: Memphis

first: Masayuki

last: Yamashita

state: TN

address: 262 Danny Thomas Place

department: Division of Experimental Hematology, Department of Hematology

institute: St. Jude Children's Research Hospital

summary: Quiescent hematopoietic stem cells (HSCs) are prone to mutagenesis, and accumulation of mutations can result in hematological malignancies. The mechanisms through which HSCs prevent such detrimental accumulation, however, are unclear. Here, we show that Aspp1 coordinates with p53 to maintain the genomic integrity of the HSC pool. Aspp1 is preferentially expressed in HSCs and restricts HSC pool size by attenuating self-renewal under steady state conditions. After genotoxic stress, Aspp1 promotes HSC cycling and induces p53-dependent apoptosis in cells with persistent DNA damage foci. Beyond these p53-dependent functions, Aspp1 attenuates HSC self-renewal and accumulation of DNA damage in p53-null HSCs. Consequently, concomitant loss of Aspp1 and p53 leads to the development of hematological malignancies, especially T-cell leukemia and lymphoma. Together, these data highlights coordination between Aspp1 and p53 in regulating HSC self-renewal and DNA damage tolerance, and suggest that HSCs possess specific mechanisms that prevent accumulation of mutations and malignant transformation.

overall_design: 8-week-old WT, Aspp1-/-, Mx1-Cre(+)p53flox/flox and Mx1-Cre(+)Aspp1-/-p53flox/flox mice were intraperitoneally administered with 400 μg pIpC five times every other day to obtain WT, Aspp1-/-, p53-/- and Aspp1-/-p53-/- bone marrow. 4 weeks after pIpC treatment, bone marrow lineage(-) Sca-1(+) cKit(+) cells were isolated. RNA was extracted and pooled from 3 independent mice per genotype. RNA samples were then amplified, labeled, and hybridized to independent arrays.

first: Eriko

last: Nitta

first: Toshio

last: Suda


title: Gene expression profiles in rat lung following intratracheal instillation with impurity-free single-wall carbon nanotubes

status: Public on Sep 17 2014

first: Katsuhide

last: Fujita

summary: To further development of our gene expression approach to assess the effects of manufactured nanomaterials at the transcriptional level, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish characterization of physicochemical properties of impurity-free single-wall carbon nanotubes (SWCNTs). We have prepared two types of dispersed the SWCNTs, namely relatively small bundles and a short linear shape (CNT-1) and large bundles and a long linear shape (CNT-2), and attempted to characterize time-dependent changes in the gene expression of lung tissues until 90 days after intratracheal instillation with SWCNTs suspensions at 0.4 mg injected dose per rat.

overall_design: Groups of nine-week-old male Wistar rats (n= 4 per group/ time point) were intratracheally instilled with single-wall carbon nanotubes (SWCNTs) suspended in 0.4 ml of 1.0mg/mL bovine serum albumin (BSA) as a single injection 0.4 mg SWCNTs/ rat. Control groups received 1.0mg/mL BSA (vehicle control). After intratracheal instillation treatment, rats were housed within polycarbonate cages at a controlled temperature of 22 °C with a chow diet ad libitum, and dissected at 1day, 3 days, 7 days, 30 days, and 90 days post-instillation. Right lungs of anesthetized rats were perfused with physiological saline, excised, and used for DNA microarray analysis.

first: Makiko

last: Fukuda


title: Molecular responses in skeletal muscles following spinal cord injury and the effect of locomotor training

status: Public on Jun 30 2015

city: Washington

first: Yi-Wen

last: Chen

state: DC

address: 111 Michigan Ave NW

institute: Children's Research Institute

summary:
Spinal cord injury (SCI) is one of the most disabling health problems facing adults today.  Locomotor training has been shown to induce substantial recovery in muscle size and muscle function in both transected and contusion injury animal models of SCI.
The overall objective of this study is to implement genome wide expression profiling of skeletal muscle to define the molecular pathways associated with muscle remodeling after SCI and during locomotor training (TM).

overall_design: We profiled rat soleus of total 36 samples including controls;  3, 8 and 14 days after SCI;  8 and 14 days after SCI with locomotor treadmill training (TM).


title: Non-genomic and Immune Evolution in Melanoma with Acquired MAPKi Resistance

last: Hugo

first: Xiangju

first: Douglas

last: Johnson

first: Jeffrey

last: Sosman


title: Gene expression profiles in rat alveolar macrophages exposure to impurity-free single-wall carbon nanotubes

status: Public on Sep 11 2014

summary: To further development of our gene expression approach to assess the effects of manufactured nanomaterials at the transcriptional level, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish characterization of physicochemical properties of impurity-free single-wall carbon nanotubes (SWCNTs), namely, relatively small bundles and a short linear shape (CNT-1) and large bundles and a long linear shape (CNT-2).

overall_design: Two kinds of the impurity-free singlewall carbon nanotubes (SWCNTs), CNT-1 or CNT-2 induced gene expression in rat alveolar macrophages were measured at 24 hours exposure to doses of 0.1mg/mL. The experiments were performed using control for each experiment (n=4).


title: Gene expression profiling of gastrocnemius of mini muscle mice

status: Public on Feb 19 2013

summary:
Few studies have investigated heterogeneity of selection response in replicate lines subjected to equivalent selection. We developed 4 replicate lines of mice based on high levels of voluntary wheel running (high runner or HR lines) while also maintaining 4 non-selected control lines. This led to the unexpected discovery of the HR mini-muscle (HRmini) phenotype, recognized by a 50% reduction in hindlimb muscle mass, which became fixed in 1 of the 4 HR selected lines.
Here, we report genome-wide expression profiling describing transcriptome differences between HRnormal and HRmini medial gastrocnemius. This work provides a resource for understanding differences in muscle phenotypes in populations exhibiting high running capacity.

overall_design: Male mice were used from an animal model of 4 closed lines selectively bred for high voluntary wheel-running behaviour (HR) and 4 control lines bred without intentional selection, described in Swallow et al. Animals used in the current work were sampled from generation 37 at a mean age of 84 days (range = 79-86). For microarray analysis, we used gastrocnemius muscles (including both lateral and medial portions) from HRmini line #3 and HRnormal line #8 (n = 6, in each group). To obtain sufficient RNA, gastrocnemius samples of HRmini were pooled from left and right limbs from each animal, whereas HRnormal gastrocnemius was sampled from either left or right limb only.


title: Gene expression profiles in rat lung following intratracheal instillation with single-wall carbon nanotubes

status: Public on Sep 07 2013

summary: Gene expression profiling of the rat lung following intratracheal instillation with single-wall carbon nanotubes (SWCNTs) was employed to gain insights into these molecular events. We attempted to characterize time-dependent changes in the gene expression until 754 days after intratracheal instillation with SWCNTs suspensions at 0.2 mg (L-SWCNT) and 0.4 mg (H-SWCNT) injected dose per rat, and to identify the shift from the acute-phase to the chronic-phase phase on the basis of evaluation at the molecular level.

overall_design: Groups of nine-week-old male Wistar rats (n= 6 per group/ time point) were intratracheally instilled with single-wall carbon nanotubes (SWCNTs) suspended in 0.4 ml distilled water including 0.1% Triton X-100 as a single injection 0.1 mg (L-SWCNT) and 0.4 mg (H-SWCNT)  SWCNTs/ rat). Control groups received 0.1% Triton X-100 (vehicle control). After intratracheal instillation treatment, rats were housed within polycarbonate cages at a controlled temperature of 22 °C with a chow diet ad libitum, and dissected at 3 days, 7 days, 30 days, 90 days, 180 days, 365 days and 754 days post-instillation. Right lungs of anesthetized rats were perfused with physiological saline, excised, and used for DNA microarray analysis.


title: CD133+ cells contain cancer stem cell-like properties in Malignant Mixed Mullerian Tumor (Carcinosarcoma) of the Uterus

status: Public on Feb 10 2013

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

institute: Toray Industries,Inc.

summary:
Cancer stem cells (CSCs) that display tumor-initiating properties have recently been identified.  We herein identify and characterize CSCs in human uterine carcinosarcoma, a highly aggressive and therapy-resistant gynecologic malignancy, which is considered to be of mesodermal origin.  FU-MMT-1, a cell-line, which was established by us (Emoto M, Cancer 1992) from a patient with uterine carcinosarcoma, was evaluated.  FU-MMT-1 contained a high population of CD133, CD44, CD90, and CD29 positive cells.
Using the magnetic bead cell separation method, we isolated CD133+ cells, which predominantly form spheres in culture. These CD133+ cells form transplantable tumors in vivo.  A qRT-PCR analysis of the genes implicated in stem cell maintenance revealed that CD133+ cells express significantly higher levels of OCT4, NANOG, and BMI-1 than CD133－ cells.  Moreover, CD133+ cells showed a high expression of PAX2 and WNT4, which are the essential genes in Mullerian duct formation.  The tumor derived from CD133+ cells replicated vimentin, ERα, ERβ, and PR expressions　of the parent tumor.  These findings suggest that CD133+ FU-MMT-1 cells have the characteristics of CSCs and Mullerian mesenchymal progenitors.

overall_design: CD133+ and CD133- population of FU-MMT-1 cells were analyzed by microarray.

first: Batsuren

last: Choijamts

first: Shiro

last: Jimi

first: Toru

first: Yasuko

last: Naganuma

first: Masahide

last: Kuroki

first: Shingo

last: Miyamoto

first: Hiroshi

last: Iwasaki

first: Emoto

last: Makoto


title: Melanoma: comparison between common nevi, radial/vertical growth phase melanoma, metastases and dysplastic nevi

status: Public on Sep 30 2009

city: Biella

first: giovanna

last: chiorino

address: via malta 3

department: Cancer Genomics

country: Italy

institute: Fondo Edo Tempia

summary:
Despite malignant cutaneous melanoma is relatively rare compared to other skin cancers, it is still responsible for 80% of all skin cancer-related deaths. To identify molecular signatures of melanoma progression, excisional biopsies from 18 common melanocytic nevi (CMN), 8 primary radial growth phase melanomas (RGPM), 15 primary vertical growth phase melanomas (VGPM) and 5 melanoma metastases (MTS) were profiled using whole genome oligo-microarrays. Differentially expressed genes for each progression step were identified, and validation of selected transcripts by qRT-PCR was performed on an independent cohort of fixed samples. The comparison between CMN and RGPM showed an enrichment of Gene Ontology (GO) terms related to inter and intra-cellular junctions, whereas the transition from RGPM to VGPM was characterized by the deregulation of WNT3, MAPK and AKT pathways. In this step, enrichment analysis underlined the alteration of biological processes linked to apoptosis. Upregulation of genes involved into DNA double-strand breaks repair and downregulation of cellular adhesion genes were observed in MTS respect to VGPM. Futhermore, the gene expression profiles of 11 dysplastic nevi (DN) were compared to all the others. Some genes controlling proliferation were found more expressed than in CMN. Overall, DN displayed an heterogeneous behaviour, with relevant oncogenes, such as MYC and BCL6, less expressed than in RGPM, and a modulation pattern similar to VGPM for a subset of gene families, such as mismatch repair. This suggests that DN is not an intermediate step within melanoma progression, but a separate entity with an independent risk of progression to melanoma

Keywords: Melanoma progression, gene expression profiling, qPCR

overall_design: In order to identify genes implicated during the course of melanoma development and progression, a total of 57 excisional biopsies from common melanocytic nevi (n = 18),  dysplastic nevi (n = 11), primary radial growth phase malignant melanomas (n = 8), primary vertical growth phase malignant melanomas (n = 15) and melanoma metastases (n = 5) were analyzed. Total RNA was isolated by using RNeasy Mini Kit (Qiagen, Dusseldorf, Germany). TotRNA quality was checked by means of RNA 6000 pico chip assays (Agilent Technologies, Palo Alto, CA) run on the Agilent 2100 bioanalyzer.   RNA isolated from each fresh tissue and from the human universal reference (BD™ Human Universal Reference Total RNA, Clontech, Palo Alto, CA) was amplified by means of the Amino Allyl MessageAmp II aRNA Kit (Ambion) to obtain amino allyl antisense RNA (aaRNA) following the method developed by Eberwine and coworkers. Two rounds of amplification were performed to obtain the necessary quantity of aaRNA for labeling. Briefly: mRNA was reverse transcribed in cDNA single strand; after the second strand synthesis (in the second round of amplification), cDNA was in vitro transcribed in aaRNA including amino allyl modified nucleotides (aaUTP). Both dsDNA and aaRNA underwent a purification step using columns provided with the kit. Labeling was performed using NHS ester Cy3 or Cy5 dyes (Amersham Biosciences, Buckinghamshire UK) able to react with the modified RNA. mRNA quality was checked by means of RNA 6000 nano chip assays (Agilent Technologies). At least 5 ug of mRNA for each sample were labeled and purified with columns. Equal amounts (0.75 ug) of labeled specimens from sample and reference were put together, fragmented and hybridized to oligonucleotide glass arrays representing 41K human unique genes and transcripts (Human Whole Genome Oligo Microarray Array, Agilent Technologies). All steps were performed using the In Situ Hybridization kit-plus (Agilent Technologies) and following the 60-mer oligo microarray processing protocol (Agilent Technologies). Then, slides were washed with the SSPE wash procedure and scanned with the dual-laser microarray scanner Agilent G2505B. For each sample, a dye-swap replicate was performed.  To visually inspect the relationships among samples, unsupervised clustering analysis was applied to the ratios between each DN, RGPM , VGPM or MTS sample and the average profile of all the CMN included into the study, just selecting transcripts with p-value less than 0.01 in at least half of the samples considered. Transcripts modulated in each progression step were then selected by applying a cut-off of 2 for the B value yielded by the limma procedure applied on original ratios (sample over common reference). Initially, DN were included into either the CMN class or the RGPM one, according to the degree of their cyto-architectural atypia However, the presence of such lesions among either CMN or RGPM made the distinction between these two classes and between RGPM and VGPM much less clear. Therefore, to prevent the increasing of heterogeneity, DN were excluded and this allowed the detection of many more differentially expressed transcripts between CMN and RGPM and, especially, between RGPM and VGPM. The great difference found between metastases and the rest of the samples was consistent with unsupervised results.  Enrichment of Gene Ontology categories (in particular, biological processes) and gene networks or cellular pathways was performed on each list by using DAVID functional annotation tool and applying a cut-off of 0.01 on the enrichment score obtained.  For each progression step, some genes previously described as differentially expressed were found. Furthermore, other novel gene transcripts, never reported as involved in melanoma progression, were identified. The expression deregulation of some of these novel genes was then confirmed on an independent cohort of samples by RT-qPCR.

first: Maria

last: Scatolini

first: Maurizia

last: MelloGrand

first: Enrico

last: Grosso

first: Tiziana

last: Venesio

first: Alberto

last: Pisacane

first: Antonella

last: Balsamo

first: Roberta

last: Sirovich

first: Mauro

last: Risio

first: Giovanna

last: Chiorino


title: Gene expression and muscle fiber function in a porcine ICU model

status: Public on Aug 31 2009

first: Yi-Wen

last: Chen

summary:
Background: Skeletal muscle wasting and impaired muscle function in response to mechanical ventilation and immobilization in intensive care unit (ICU) patients are clinically challenging partly due to (i) the poorly understood intricate cellular and molecular networks; and (ii) the unavailability of an animal model mimicking this condition. By employing a unique porcine model mimicking the conditions in the ICU with long-term mechanical ventilation and immobilization, we have analyzed the expression profile of skeletal muscle biopsies taken at three time points during a five-day period.
Results: We have analyzed the expression profile of skeletal muscle biopsies taken at three time points during a five-day period. Among the differentially regulated transcripts, extracellular matrix, energy metabolism, sarcomeric proteins and LIM protein mRNA levels were down-regulated while ubiquitin proteasome system, cathepsins, oxidative stress responsive genes and heat shock proteins (HSP) mRNAs were up-regulated
Conclusions: We conclude that induction of HSPs may play an inherent temporary protective mechanism in skeletal muscle in the early stages of immobilization and mechanical ventilation. The proposed molecular events leading to our final hypothesis are illustrated in the manuscript.

Keywords: Treatment, immobilization, muscle function.

overall_design: Sixteen female domestic piglets (Sus scrofa, average body weight 26.5 kg) were used in this study. All piglets were immobilized by anesthesia and mechanically ventilated (Servo 900C, Siemens-Elema, Solna, Sweden). The first m. biceps femoris biopsies (day 1)  were obtained from all animals, after administering anesthetics. During the five day study period, four  animals were sedated using isoflurane inhalation (Abbott Laboratories, Chicago, Il, USA, 0.8 – 1.3% end-tidal concentration) supplemented by intravenous bolus doses of morphine and ketamine as needed. Biopsies from the m. biceps femoris were obtained on two further separate occasions (days 3 and 5) in these animals. Core body temperature (blood) was maintained in the range of 38.5 – 40°C by a servocontrolled heating pad.  The animals received intravenous crystalloid fluid (Ringer’s acetate) to maintain stable blood pressure and urinary output and a glucose infusion (Rehydrex, Fresenius Kabi, Stockholm, Sweden, 25 mg glucose /mL) in the range of 0.5 – 1.5 mg/kg/minute to decrease the effects of catabolism.  Each animal received prophylactic streptomycin 750 mg/d and benzylpenicillin 600 mg/d (Streptocillin Vet, Boeringer-Ingelheim, Hellerup, Denmark). Arterial blood gas analysis as well as electrolytes and blood glucose levels were monitored regularly and kept in the normal range throughout the study period.

first: Lars

last: Larsson

first: Varuna

last: Banduseela

first: Julien

last: Ochala

first: Rongye

last: Shi

first: Hanna

last: Goransson

first: Holly

last: Norman

first: Peter

last: Radell

middle: I

last: Eriksson

first: Eric

last: Hoffman


title: Gene expression in articular cartilage - subchondral bone of FRZB knockout mice

status: Public on Jan 12 2012

city: Leuven

first: Rekin's

last: Janky

address: Herestraat 49 Box 816

department: Nucleomics Core

country: Belgium

institute: VIB

summary:
Objective : To study molecular changes in the articular cartilage and subchondral bone of the tibial plateau from mice deficient in frizzled related protein (Frzb) compared to wild-type mice by transcriptome analysis.
Methods : Gene-expression analysis of the articular cartilage and subchondral bone of 3 wild-type and 3 Frzb-/- mice was performed by microarray. Pathway analysis of differentially expressed genes between 3 wild-type and 2 Frzb-/- samples  was explored with PANTHER, DAVID and GSEA bioinformatics tools. Activation of the WNT pathway was analyzed using western blot. The effects of Frzb gain and loss of function on chondrogenesis and cell proliferation was examined using ATDC5 micromasses and mouse ribcage chondrocytes.
Results : Extracellular matrix-associated integrin and cadherin pathways, as well as WNT pathway genes were upregulated in Frzb-/- samples. Several WNT receptors, target genes, and other antagonists were upregulated, but no difference in active β-catenin was found. Analysis of ATDC5 cell micromasses overexpressing FRZB indicated an upregulation of aggrecan and Col2a1, and downregulation of molecules related to damage and repair in cartilage, Col3a1 and Col5a1. Silencing of Frzb resulted in downregulation of aggrecan and Col2a1. Pathways associated with cell cycle were downregulated. Ribcage chondrocytes derived from Frzb-/- mice showed decreased proliferation compared to wild-type cells.
Conclusions : Our analysis provides evidence for tight regulation of WNT signaling, shifts in extracellular matrix components and effects on cell proliferation and differentiation in the articular cartilage - subchondral bone unit in Frzb-/- mice. These data further support an important role for FRZB in joint homeostasis and highlight the complex biology of WNT signaling in the joint.

first: Liesbet

last: Lodewyckx

first: Frederic

last: Cailotto

first: Sarah

last: Thysen

first: Frank

middle: P

last: Luyten

first: Rik

middle: J

last: Lories


title: Common Gene Transcriptional Patterns Following Immobilization, Spinal Cord Injury, and Unloading in Human Skeletal Muscle

status: Public on Oct 23 2010

summary:
Following spinal cord injury, skeletal muscle loss is rapid. This severe atrophy is attributed to declines in protein synthesis and increases in protein breakdown. However, the signaling mechanisms controlling these changes are not well understood. Nine male patients and one female patient with spinal cord injury (SCI) (Mean ± SEM = 43.9 ± 6.7 yrs) were recruited for this study. Six patients were quadriplegics and four patients were paraplegics. Inclusion criteria were as follows: patients above the age of 18 yrs, absence of severe brain injury (Glasgow Coma Scale > 13), absence of muscle-crush injury or compartment syndrome, absence of all of the following conditions: hypoxic injury, systemic sepsis, systemic inflammatory or autoimmune disease, and malignancy. Muscle biopsies were obtained from the vastus lateralis muscles of the SCI patients two days and five days post-SCI. Biopsies collected two days post-SCI were included in the current analysis.  Expression changes were measured by microarray and gene clustering; identification of enriched functions and canonical pathways were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) and Ingenuity Pathway Analysis (IPA).
Functional analysis found that 48h following SCI expression, gene expression changes were related to decreases in metabolic functions such as the tricarboxylic acid cycle and oxidative phosphorylation as well as increases in functions associated with protein degradation such as proteasome activity and ubiquitination.  Furthermore, increases in expression of metallothioneins were found to be the most over-represented functional group in the DAVID analysis. Results from this study showed that functional categories of gene expression changes in human skeletal muscle are consistent with previous findings in animals.

overall_design: Muscle biopsies were obtained from the vastus lateralis muscles of the SCI patients two days and five days post-SCI. (N = 10). A 5mm Berstrom biopsy needle was used. Biopsy samples were immediately snap-frozen in liquid nitrogen upon excision. All samples were stored at -80° C until analysis.

first: Kimberly

last: Reich

first: Maria

middle: L

last: Urso

first: Paul

middle: D

last: Thompson

first: Priscilla

last: Clarkson


title: Gene expression data in CD4+ and CD8+ cells in sarcoidosis patients following antimycobacterial therapy

status: Public on Jul 23 2013

city: Pittsburgh

first: Kusum

middle: Vijay

last: Pandit

state: PA

address: 200, Lothrop street, W1200-25A Biomedical Science Tower

department: Medicine-PACCM

institute: University of Pittsburgh

summary: Many chronic cutaneous diseases associated with microbial antigens demonstrate clinical progression due to T cell hyporesponsiveness. Appropriate antimicrobial therapy restores T cell function, leading to clinical resolution.  Due to the association of sarcoidosis with mycobacterial antigens, we compared the efficacy of antimycobacterial therapy with placebo in chronic cutaneous sarcoidosis.

overall_design: We conducted a randomized, placebo-controlled, single-blind trial on chronic cutaneous sarcoidosis subjects.  Participants received the oral CLEAR regimen:  Levofloxacin 750 mg on day 1, then 500 mg daily, Ethambutol 1200 mg daily, Azithromycin 500 mg on day 1, then 250 mg daily, and Rifampin 300 mg daily, or a comparative placebo regimen, for a total of 8 weeks, with a 180 day follow-up.  Participants were monitored for absolute change in lesion diameter and decrease in granulomas burden upon completion of therapy.

middle: V

first: Wonder

last: Drake

first: Naftali

last: Kaminski


title: Skeletal muscles of untreated children with juvenile dermatomyositis

status: Public on Jul 18 2008

first: Yi-Wen

last: Chen

summary:
Background :To evaluate the impact of the duration of chronic inflammation on gene expression in skeletal muscle biopsies (MBx) from untreated children with juvenile dermatomyositis (JDM) and identify genes and biological processes associated with the disease progression, expression profiling data from 16 girls with active symptoms of JDM greater or equal to 2 months were compared with 3 girls with active symptoms less than 2 months.
Results: Seventy-nine genes were differentially expressed between the groups with long or short duration of untreated disease.  Genes involved in immune responses and vasculature remodeling were expressed at a higher level in muscle biopsies from children with greater or equal to 2 months of symptoms, while genes involved in stress responses and protein turnover were expressed at a lower level.  Among the 79 genes, expression of 9 genes showed a significant linear regression relationship with the duration of untreated disease.  Five differentially expressed genes--HLA-DQA1, smooth muscle myosin heavy chain, clustering, plexin D1 and tenomodulin--were verified by quantitative RT-PCR.  The chronic inflammation of longer disease duration was also associated with increased DC-LAMP+ and BDCA2+ mature dendritic cells, identified by immunohistochemistry.
Conclusions: We conclude that chronic inflammation alters the gene expression patterns in muscle of untreated children with JDM.  Symptoms lasting greater or equal to 2 months were associated with dendritic cell maturation and anti-angiogenic vascular remodelling, directly contributing to disease pathophysiology.

Keywords: Disease progression; time course

overall_design:
After obtaining informed consent, 23 girls with definite JDM were enrolled in this study prior to obtaining the MRI directed diagnostic muscle biopsy.  All 23 JDM samples and 4 healthy age- and sex-matched controls were expression profiled and for first gene filtering.  Only profiling data from untreated patients (19 profiles) were then analyzed statistically.
disease duration : less than 2 months: YJD-JDM-2UA-s2,YJD-JDM-1UA-s2,YJD-JDM-16UA-s2
disease duration : more than 2 months:YJD-JDM-30UA-s2,YJD-JDM-19UA-s2,YJD-JDM-5UA-s2,YJD-JDM-21UA-s2,YJD-JDM-18UA-s2,YJD-JDM-3UA-s2,YJD-JDM-23UA-s2,YJD-JDM-9UA-S2,YJD-JDM-12UA-s2,YJD-JDM-14UA-s2,YJD-JDM-25UA-s2,YJD-JDM-8UA-s2,YJD-JDM-15UA-s2,YJD-JDM-13UA-s2,YJD-JDM-10UA-S2,YJD-JDM-6UA-s2.

first: Rongye

last: Shi

first: Nicholas

last: Geraci

first: Sheela

last: Shrestha

first: Heather

last: Gordish-Dressman

first: Lauren

last: Pachman


title: Gene expression profiles in human alveolar epithelial cell line exposure to impurity-free single-wall carbon nanotubes

status: Public on Sep 25 2012

first: Katsuhide

last: Fujita

summary: To further development of our gene expression approach to assess the effects of manufactured nanomaterials at the molecular level, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish characterization of physico-chemical properties of impurity-free single-wall carbon nanotubes (SWCNTs).

overall_design: Three kinds of single-wall carbon nanotubes (SWCNTs), CNT-1, CNT-2 or CNT-3 induced gene expression in human alveolar epithelial cell lines were measured at 24 and 48 hours exposure to doses of 90.8μg/mL (CNT-1), 109.0μg/mL (CNT-2), and 77.0μg/mL (CNT-3). Three independent experiments were performed at each time (24 or 48 hours) using different untreated control for each experiment (n=4).

first: Makiko

last: Fukuda


title: Expression profiling data of RD and C2C12 cells ectopically expressing DUX4

status: Public on Apr 08 2013

summary:
Transcriptomic changes induced by DUX4 expression were compared between human and mouse cell lines of muscle lineage.
We used microarrays to compare transcripts induced in human rhabdmyosarcoma and mouse C2C12 cells ectopically expressing DUX4.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Human rhabdomyosarcoma and mouse C2C12 cells were transfected with DUX4 expression vectors (n=4).  Cells transfected with insertless vectors were used as controls.  Samples were processed for RNA extraction 16 hours following transfection.


title: Gene expression profiles in rat lung following intratracheal instillation with C60 fullerene particles

status: Public on Aug 26 2009

summary: Gene expression profiling of the rat lung following intratracheal instillation with C60 fullerene particles was employed to gain insights into these molecular events.

overall_design: Groups of nine-week-old male Wistar rats (n= 4-6 per group/ time point) were intratracheally instilled with C60 fullerene suspended in 0.4 ml distilled water including 0.8% Tween-80 as a single injection (0.1 mg, 0.2 mg (LD: low dose) and 1.0 mg (HD: high dose) C60 fullerene/ rat). Control groups received 0.8% Tween-80 (vehicle control). After intratracheal instillation treatment, rats were housed within polycarbonate cages at a controlled temperature of 22 °C with a chow diet ad libitum, and dissected at 3 days, 1 week, 1 month, 3 month, and 6 month post-instillation. Right lungs of anesthetized rats were perfused with physiological saline, excised, and used for DNA microarray analysis.

first: Hitoshi

last: Iwahashi


title: Gene expression profiles in rat lung after inhalation exposure to C60 fullerene or ultrafine NiO particles

status: Public on Oct 23 2008

summary: Gene expression profiling of the rat lung after whole-body inhalation exposure to C60 fullerene and ultrafine nickel oxide (Uf-NiO) particles as a positive control were employed to gain insights into these molecular events.

overall_design: Groups of 9-week-old male Wistar rats (n = 5 per group/time point) were exposed to clean air (negative control), C60 fullerene or Uf-NiO (positive control) suspension in a whole-body exposure chamber. Rats were exposed to aerosol for 6 hours a day, for 4 weeks (5 days a week). Standard chow diet was provided ad libitum during non-exposure hours. After exposure period for 4 weeks, rats were housed within polycarbonate cages at a controlled temperature of 22 °C with a chow diet ad libitum, and dissected at 3 days and 1month (33 days) post-exposure. Lungs of anesthetized rats were perfused with physiological saline, excised, and used for C60 fullerene or nickel burdens in lungs (n = 4, left lungs), TEM analysis (n = 1, whole lungs) and microarray analysis (n = 4, right lungs).


title: Gene expression profiles in human keratinocytes exposure to ultrafine, fine, and submicron TiO2 particles

status: Public on Jun 15 2009

summary: Gene expression profiling of the human keratinocytes cell line (HaCaT)  exposure to ultrafine, fine, and submicron TiO2 particles were employed to gain insights into the molecular events.

overall_design: Three types of bulk TiO2 anatase particles, ST-01(average primary particle size= 7nm,  specific surface area = 316m2/g), ST-21(20nm and 66m2/g), and ST-41(200nm and 10m2/g) used in this study were purchased from Ishihara Sangyo Kaisha Ltd., Japan. TiO2 particles were dispersed and size-fractionated in Dulbecco’s modified Eagle’s medium (DMEM) . TiO2 particles was dispersed in heat-inactivated fetal bovine serum (FBS) and centrifuged at 16,000 x g for 20 min. Removing the supernatant, the pellet was washed with DMEM, and centrifuged at 16,000 x g for 20 min. The supernatant was removed and dispersed in fresh DMEM with 10 % FBS medium and antibiotic/antifungal-agent (100 units/ml of penicillin, 100 μg/ml of streptomycin, and 250 ng/ml of amphotericin B) defined as DMEM-FBS medium, and centrifuged at 8,000 x g for 20 min. Removing the supernatant, the pellet was vortexed with fresh DMEM-FBS medium and centrifuged at 4,000 x g for 20min. The supernatant of 4,000 x g fraction was collected. Continuously, the centrifugal force was reduced to 2,000 x g, 1,000 x g and 500 x g. Each supernatant of 2,000 x g, 1,000 x g, and 500 x g fraction was collected. The 500 x g fraction supernatant was 0.8 µm membrane-filtered. The concentrations and the secondary average diameter of TiO2 particles in the supernatant fractions were individually characterized using X-ray diffraction (XRD), dynamic light scattering (DLS), and transmission electron microscopy (TEM) at 120 kV. The samples were defined as T-7 (ST-01, 4,000 x g fraction), T-20 (ST-21, 1,000 x g fraction), and T-200 (ST-41, 500 x g fraction), and were utilized for the following DNA microarray analysis. Human keratinocyte cells (HaCaT) purchased from the German Cancer Research Center (DKFZ) were cultured in DMEM-FBS medium at 37 °C in a humidified atmosphere of 5% CO2 and 95% air The passage numbers 2–10 were used in the experiments, and cells were seeded at a density of approximately 2 x 10^5 cells/ml. All experiments were performed in triplicate (n=3).


title: Effects of 48h Lower Limb Unloading in Human Skeletal Muscle

summary:
Although short-term disuse does not result in measurable muscle atrophy, studies suggest that molecular changes associated with protein degradation may be initiated within days of the onset of a disuse stimulus. We examined the global gene expression patterns in sedentary men (n = 7, mean age ± S.D = 22.1 ± 3.7 yr) following 48h unloading (UL) via unilateral lower limb suspension and 24h reloading (RL). Biopsy samples of the left vastus lateralis muscle were collected at baseline, 48h UL, and 24h RL. Expression changes were measured by microarray and gene clustering; identification of enriched functions and canonical pathways were performed using the Database for Annotation, Visualization and Integrated Discovery (DAVID) and Ingenuity Pathway Analysis (IPA). Four genes were validated with qRT-PCR, and protein levels were measured with Western blot. Of the upregulated genes after UL, the most enriched functional group and highest ranked canonical pathway were related to protein ubiquitination. The oxidative stress response pathway was the second highest ranked canonical pathway. Of the downregulated genes, functions related to mitochondrial metabolism were the mostly highly enriched. In general, gene expression patterns following UL persisted following RL. qRT-PCR confirmed increases in mRNA for UPP-related E3 ligase Atrogin1 (but not accompanying increases in protein products) and stress response gene heme oxygenase-1 (HMOX,  which showed a trend towards increases in protein products at 48h UL) as well as extracellular matrix (ECM) component COL4.
The gene expression patterns were not readily reversed upon RL suggesting that molecular responses to short-term periods of skeletal muscle inactivity may persist after activity resumes.

overall_design: Biopsies were taken of the left vastus lateralis of healthy, sedentary men (N = 7) at baseline, immediately following 48h UL and 24h RL. A 5mm Berstrom biopsy needle was used. Biopsy samples were immediately snap-frozen in liquid nitrogen upon excision. All samples were stored at -80° C until analysis.

first: Yi-wen

first: Eric

last: Hoffman