Biology of human melanoma
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Waleska Martins
PROVIDER: E-GEOD-17275 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Gene network analyses point to the importance of human tissue kallikreins in melanoma progression.
Martins Waleska K WK Esteves Gustavo H GH Almeida Otávio M OM Rezze Gisele G GG Landman Gilles G Marques Sarah M SM Carvalho Alex F AF L Reis Luiz F LF Duprat João P JP Stolf Beatriz S BS
BMC medical genomics 20111027
<h4>Background</h4>A wide variety of high-throughput microarray platforms have been used to identify molecular targets associated with biological and clinical tumor phenotypes by comparing samples representing distinct pathological states.<h4>Methods</h4>The gene expression profiles of human cutaneous melanomas were determined by cDNA microarray analysis. Next, a robust analysis to determine functional classifications and make predictions based on data-oriented hypotheses was performed. Relevant ...[more]
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Project description:This SuperSeries is composed of the following subset Series: GSE18020: Gene expression profile of N+ and N0 HNSCC GSE22055: Gene expression profile of recurrent and non-recurrent HNSCC Refer to individual Series
2010-06-10 | E-GEOD-22243 | biostudies-arrayexpress
Project description:Head and neck squamous cell carcinomas (HNSCCs) is the seventh most common solid malignancy in the United States, accounting for more than 47,000 new cancer cases. HNSCC shows significant diversity in its clinical behavior after treatment, which cannot be predicted using the current clinical or pathological markers. Despite tumor complexity, many studies have tried unsuccessfully to test single genes to be used as prognostic markers in HNSCC. A group of tumor samples can be characterized in terms of the behavior of modules. These modules include clusters of coexpressed genes, such as genes that belong to the same pathway or functional category. Cancer is a multifaceted phenomenon that involves activation and/or disruption of various cellular processes. Thus, the identification of pathways or group of genes such as those involved in the development of lymph node metastasis and recurrent disease may help understanding the complex biology of cancer. Samples were obtained during surgery and neck dissection of 47 patients with primary untreated HNSCC at the Head and Neck Surgery Department from the Hospital AC Camargo (São Paulo, Brazil) between 1998 and 2003. Diagnosis of HNSCC was determined by biopsy. All patients signed a pre-informed consent and the study was approved by our institutional review board. After surgery, all patients were treated with adjuvant radiotherapy. Recurrence were diagnosed by imaging or biopsy. Tumor samples were snap-frozen in liquid nitrogen. Before RNA extraction, diagnosis was confirmed by hematoxylin-eosin staining. Frozen samples were hand dissected for removal of normal cells, necrosis, and infiltrating inflammatory cells. Total RNA was extracted using TRIzol. RNA quality was accessed by spectrophotometry and gel electrophoresis. To be considered as high-quality, the RNA had to have a 260/280 ratio higher than 1.7 and a 18S/28S rRNA ratio ~2. Amplifictaion of the mRNA was done using a T7-based protocol and cDNA was indirectly labeled with Alexa Dye 555 or 647. Samples and a common RNA reference were hybridized overnight at 42oC in dye-swap to a 4,800-element in-house printed microarray, enriched with cancer-related ESTs derived from the Human Cancer Genome Project. After washing, slides were scanned on a confocal laser scanner and data were extracted.
2010-06-10 | E-GEOD-22055 | biostudies-arrayexpress
Project description:Cutaneous melanomas are malignant radio and chemoresistant neoplasias presenting high morbidity and elevated mortality rates. Isolated Limb Perfusion (ILP) with Melphalan (Mel) is used in the treatment of non-resectable locally advanced melanomas of extremity sparing the limb from amputation in 40-50% of the cases. Adding the Tumor Necrosis Factor alpha (Tnfa) improves total complete response to 70-90%. The cellular and molecular mechanisms underlying the changes promoted by Mel and Tnfa are not completely understood. In this study we evaluated the impact of systemic Mel and Tnfa administration on tumor growth, analyzed the morphological changes promoted by each treatment, and searched for early molecular targets of Mel and Tnfa, alone or in combination, in a murine melanoma model. Morphological changes were analyzed by histological analysis, while microarray gene expression followed by quantitative RT-PCR were used to search for early molecular targets. We found that Mel systemic administration accounted for the impairment of tumor-growth (p<0.001) and improvement of survival. Tnfa co-administration augmented necrosis (p<0.024) and decreased mitotic rates (p=0.001). We identified a set of 118 potential molecular markers that might be correlated with the observed biologic response to treatment with Melphalan and Tnfa and which could represent potential therapeutic targets in melanoma. We used amplified RNA (aRNA) from 18 tumor samples (Control – 5 samples; Mel – 4 samples; Tnfa – 4 samples; and Mel+Tnfa – 5 samples). For replica hybridization with dye swap, aRNA from the tumors and from a pool composed of equal amounts of RNA extracted from the K1735M2, M2R, B16F10, and B16F1 melanoma cells were labeled with Alexa555 or Alexa647. Labeled aRNA samples were hybridized against a glass platform containing 16,128 immobilized sense oligonucleotides (Fox Chase Cancer Center, USA) corresponding to murine genes. Slides were pre-hybridized at 42ºC for approximately 6 hours in a solution containing Denhardt’s 5X (Ficoll 400 0.05g/mL, poli-vynil-pyrrolidone 0.05g/mL, bovine serum albumin 0.05g/mL), SSC (sodium saline citrate) 5X, 0.2% SDS (Sigma), and 1% BSA. For hybridization, we used a mix of 3.5µg of each labeled sample aRNA and reference aRNA. The hybridization solution contained Denhardt’s 5X, formamide 25% (Sigma), SSC 5X, SDS 0.1%, salmon sperm DNA 0.1mg/mL (GE Healthcare), Poly-A 0.1mg/mL (GE Healthcare), and Cot-1 0.1mg/mL (GE Healthcare), to a final volume of 100µL. Hybridizations were carried out on a Gene Tac hybridization station (Genomic Solutions) at 42ºC for about 16h. The slides were removed from the hybridization cassettes directly to a recipient containing a washing solution (SSC 2X, SDS 0.1%) at 42ºC, put in a slide rack, transferred to another recipient containing fresh solution, and washed under constant agitation at 42ºC for 5 min. After that, they were washed twice for 5min in a second wash solution (SSC 0.1X, SDS 0.1%) at room temperature and rinsed five times for 1min at room temperature with a SSC 0.1X solution. The slides were dried upside down in a centrifuge at 1500rpm for 5min. The slides were scanned with a confocal laser scanner (ScanArrayTM Express, Perkin-Elmer Life Sciences, USA), and the spot intensities processed with the help of the ScanArray Express program (Packard BioScience), with a 10µm resolution and a PMT of 60% for Alexa 555 and of 70% for Alexa 647. Each slide generated a data set for each channel corresponding to the dyes Alexa 555 and Alexa 647. The slides were scanned with a confocal laser scanner (ScanArrayTM Express, Perkin-Elmer Life Sciences, USA) with a 10µm resolution and a PMT of 60% for Alexa 555 and of 70% for Alexa 647, and data were extracted with ScanArray Express software (Packard BioScience) using the histogram method. Each slide generated a data set for each channel corresponding to the dyes Alexa 555 and Alexa 647. The Locally Weighted Scatter-plot Smoothing method (LOWESS), adjusted for linear and non-linear systematic variations, both of the intensity dependent type, mainly for low intensity spots, was employed for data normalization.
2011-12-31 | E-GEOD-21559 | biostudies-arrayexpress
Project description:Wilms tumor (WT), the commonest renal tumor of the childhood, is originated from pluripotent metanephric blastemal cells resulting in tumors with triphasic histology, composed by blastemal, epithelial, and stromal cells. Histological subtype and tumor stage have long been recognized as important prognostic factors and used for the current therapeutic approach with blastema considered as the component with the highest clinical impact. Current clinical and molecular research is directed toward identifying prognostic factors for both purposes, definition of the minimal or intense required therapy for successful treatment of children with low or high risk of relapse, respectively. In this study, to identify molecular prognostic markers predictive of tumor relapse, samples from 26 advanced (Stage III or IV) blastemal WT, whose patients presented (13 samples) or did not present (13 samples) relapse, were interrogated by 4,608 human genes immobilized in a customized cDNA platform. This analysis revealed a set of 69 differentially expressed genes, where the nine top genes were evaluated by qRT-PCR in the initial WT samples. TSPAN3, NCOA6, CDO1, MPP2 and MCM2 were technically confirmed showing down-regulation in relapse WT. TSPAN3 and NCOA6 were validated in an independent sample group. Gene trios containing these two genes combined with one of the remaining three reported a reasonable capability of discriminating relapse and no-relapse WT. Negative protein expression of MCM2 and NCOA6 was observed in around 62% and 72% of 34 independent stage III and IV WT patients, respectively without association with relapse. However, a significant association between MCM2 negative staining and chemotherapy as first treatment was observed suggesting that MCM2 protein expression is implicated anyhow with chemotherapy treatment in WT. Twenty-six blastemal-enriched advanced stage (III or IV) WT samples from sporadic and favorable histology WT were received from Children Oncology Group (COG) and used were used for microarray experiments, from which 13 samples were from patients without relapse in 5 years of follow up. Tumors were taken from primary nephrectomy at the time of initial diagnosis. Blastemal histological component was isolated following protocol described in Maschietto et al. (2008). Only samples with >80% of blastemal cells were used. Total RNA was isolated using TRIzol (Sigma) according to manufacturer´s instructions. RNA quantity and integrity was assessed by spectrophotometry (Nanodrop) and microfluidics-based electrophoresis (Agilent 2100 Bioanalyzer, Agilent), respectively, selecting only RNA samples with OD around 2.0 and RIN>5.0. A two-round RNA amplification procedure (Gomes et al. 2003) was carried out for all samples. Labeled cDNA was generated in a reverse transcriptase reaction using 4 ug of amplified RNA (aRNA), random hexamer primer (Invitrogen Life Technologies, Carlsbad, CA), Alexa-3 or 5-labeled dCTP (Amersham, Biosciences) and IMPROM (PROMEGA) using oligo-dT7(24), following manufacture recommendations. Five µg of test and reference cDNA reverse color Alexa-labeled aRNA targets were competitively hybridized against the cDNA probes in a customized cDNA platform with 4,608 ORESTES representing human genes. Dye-swap was performed for each sample as control for dye bias and used as replicate. Pre-hybridization and hybridization were performed as described (Maschietto et al. 2008). A pool of RNAs obtained from 15 distinct human cell lines as was used as reference. Signal intensities capture and analysis were performed as described in Maschietto et al (2008).
2011-06-01 | E-GEOD-22696 | biostudies-arrayexpress
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2008-04-04 | E-GEOD-11042 | biostudies-arrayexpress
Project description:Unravel the mechanisms underlying brain aging and Alzheimer´s disease (AD) has been difficult because of complexity of the networks that drive these aging-related changes. Analysis of the gene expression in the brain is a valuable tool to study the function of the brain under normal and pathological conditions. Gene microarray technology allows massively parallel analysis of most genes expressed in a tissue, and therefore is an important research tool that potentially can provide the investigative power needed to address the complexity of brain aging and neurodegenerative processes. One of the reasons that account for the resistance of AD pathogenesis to analysis is that clinically normal subjects may exhibit considerable AD pathology, blurring criteria for distinguishing subjects with normal aging or AD. Here, we analyzed hippocampal and cortex frontal gene expression from 32 subjects separated in individuals presenting, 1) both pathologic and clinical AD (definitive AD); 2) AD pathology and normal clinic (pathologic AD); 3) cognitive impairment, without AD pathology (others dementias); and 4) no cognitive impairment, without AD pathology (normal individuals). Our results show that based on gene expression profile these individuals we could verify similarity between the definitive AD group and the group that only had AD-type pathology (pathologic AD). Specimens of hippocampus and cortex frontal used in this study were obtained at autopsy from 32 subjects. Neuropathology, specifically NFT and NP, was assessed in accordance to the Braak staging and CERAD scores, respectively. Based on pathologic and clinic criteria, subjects were categorized into four groups: 1) nine subjects with AD neuropathologic (Braak = IV / V / VI and CERAD ≠ 0) presenting cognitive impairment (CDR ≥ 1), termed “definitive AD” (dAD); 2) five subjects with AD neuropathologic (Braak = IV / V / VI and CERAD ≠ 0) and without cognitive impairment (CDR = 0), termed “pathologic AD” (pAD); 3) nine subjects without AD neuropathologic (Braak = 0 / I / II and CERAD ≠ C) presenting cognitive impairment (CDR ≥ 1), termed “other dementias” (OD); 4) - nine subjects without AD neuropathologic (Braak = 0 / I / II and CERAD ≠ C) and without cognitive impairment (CDR = 0), termed “normal” (N). RNA isolation and Amplification. From total RNA, a two-round linear amplification procedure (T7-based protocol) was carried out for all samples and for a pool of RNAs obtained from 15 distinct human cell lines used as reference. Labeled cDNA was generated in a reverse transcriptase reaction using amplified RNA (aRNA). Equal amounts of test and reference cDNA reverse color Cy-labeled aRNA targets were competitively hybridized against the cDNA probes in a customized cDNA platform with 4,608 ORESTES representing human genes. Dye-swap was performed for each sample as control for dye bias and used as replicate.
2013-01-11 | E-GEOD-13214 | biostudies-arrayexpress
Project description:Acute expression of E7 oncogene from HPV-16 or HPV-18 is sufficient to overcome tumor necrosis factor-alfa (TNF) cytostatic effect on primary human keratinocytes. In the present study we investigated the molecular basis of E7-induced TNF resistance through a comparative analysis of the effect of this cytokine on the proliferation and global gene expression of organotypic cultures of normal and E7(wild type or mutant)-expressing keratinocytes. In order to determine the effects of E7 expression on TNF response, we performed 3 independent experiment for each cell line. Organotypic cultures of normal and E7(wild type or mutant)-expressing keratinocytes were treated with 2 nM TNF for 72 hours, or left untreated.
2010-06-24 | E-GEOD-17892 | biostudies-arrayexpress
Project description:We analysed 102 sample of mesenchymal tumors of different histological type and biological behaviour. The aim of the study was to identify genes related to each characteristic analysed. We compared the gene expression profiles of 102 mesenchymal tumors with histological and clinical parameters. Total RNA was extracted, amplified and spotted on cDNA microarray slides. Experiments were performed in duplicate, using the dye-swap method.
2010-06-25 | E-GEOD-14541 | biostudies-arrayexpress
Project description:Gene expression analyses through cDNA microarray of fifteen gastrocnemius muscles from transgenic and wild-type SOD1G93A mouse model by the ages of 40 and 80 days old were performed. We used a customized cDNA array containing the cDNA platform comprised of 2352 spots, 326 of them orthologous to mouse, 1384 additional human cDNA sequences, 496 negative controls (DMSO) and 48 positive controls (the Q gene from M-NM-;-phage). Gene expression results for SOD1G93A and WT age matched mice pointed to eight up- (LOXL2, PIK4CA, FZD9, CUL1, CTNND1, SNF1LK, PRKX, DNER) and nine down-regulated genes (PIK3C2A, RIPK4, ID2, C1QDC1, EIF2AK2, RAC3, CDS1, INPPL1, TBL1X) at 40 days and also to one up- (PIK3CA) and five down-regulated genes (CD44, EEF2K, FZD2, CREBBP, PIKI3R1) at 80 days. Based on differentially expressed genes, analyses for gene priorization were performed and used to construct a network of protein-protein interaction. The network based on the genes of 40 and 80 days old mice was composed by 251 and 531 genes, respectively. GRB2 and SRC were identified as central genes of both networks. In conclusion, changes in gene expression of skeletal muscle from transgenic ALS mice in pre-symptomatic periods give further evidence of early neuromuscular abnormalities that precede motor neuron death. We performed gene expression analyses by customized cDNA array, using reference design, of fifteen gastrocnemius muscles from transgenic and wild-type SOD1G93A mouse model by the ages of 40 and 80 days old. These differentially expressed lists were submitted to analyses for gene priorization and used to construct a network of protein-protein interaction.
2014-01-22 | E-GEOD-40328 | biostudies-arrayexpress
Project description:Precise regulation of transduction signaling pathways genes is crucial for correct differentiation of kidney cells and perturbation may lead to tumor onset. Wilms tumors (WT), or nephroblastoma, originates from the metanephric blastema cells, which were unable to complete the differentiation, resulting in a triphasic tumor composed by distinct cell types, blastemal, epithelial and stromal, where the former harbor molecular characteristics similar to cells of the earliest stages of kidney development. In this study, to identify key early events involved in the disruption of correct cell signaling during kidney differentiation that can drive WT, we developed a cDNA platform containing genes from signaling transduction pathways. By using bioinformatics tools, we defined high conserved regions between human and mouse orthologous genes and assessed the gene modulation in blastemal cells captured from WT and differentiated kidneys (DK) in human and from four temporal stages of kidney differentiation in mouse. We found 18 genes, whose transcriptional level of the earliest phases of blastemal cell differentiation was recapitulated in WT. PAX2, FZD10, SHPK, WNT5B, FZD2, CRABP2, FRZB, GRK7, TESK1, HDGF and IGF2 were up- and MAPK9, PIK3CA, FRAT2, ITPR3, CDH6, HIPK1 and TIMP3 were down-regulated in WT respectively. Hierarchical clustering based on the expression of this gene set grouped DK from both species, human and mouse, and discriminated them from fetal kidney and WT in human, and the earliest kidney stages in mouse, validating the model proposed by this study and reveling a transduction signaling signature of WT. High robustness of this data was detected since expression level was tested by quantitative RT-PCR in the initial and independent sample set, with 75 and 56% of agreement. Agreement of 62% was also observed in protein level assessing blastemal component of an independent group of 137 WT. Protein expression of CRABP2, IGF2, GRK7, TESK1, HDGF, WNT5B, FZD2 and TIMP3 was also characterized in human fetal kidneys revealing interesting aspects of kidney differentiation. This study identified key genes modulated during kidney differentiation which may play a determinant role for WT onset. As far as we know, FZD10, FRZB, HDGF, MAPK9, FRAT2, SHPK, WNT5B, GRK7, TESK1, HDGF, PIK3CA, ITPR3, HIPK1 and TIMP3 were not previously associated to WT. The strong connection between nephrogenesis and WT highlights the importance of a detailed characterization of modulated genes belonged to signal transduction. Identification of gene expression involved in kidney differentiation arresting might be imperative to point out early alterations that drive WT onset and consequently are potential candidate as molecular marker. Here, we characterized expression pattern of genes belonged to transduction signaling pathways in blastemal cells during kidney development stages in mouse and WT in human. For that, we established a model of inter- and intra-specific hybridization to assess gene expression modulation to identify key events that drive WT onset. Dye-swap was performed for each sample as control for dye bias and used as replicate. In total, 24 frozen favorable histology WT and differentiated kidney samples were laser microdisscted for blastemal cells. Three kidneys from CD1 lineage from Mus Musculus were isolated from embryos (E) and postnatal animals (P) at ages E15.5, E17.5, P1.5 and P7.5 for laser microdissection of the blastemal cells in all stages of kidney differentiation. NA were purified with PicoPure™ RNA Isolation kit (Arcturus Engineering #KT0204) and treated with RNase-Free DNase Set (Qiagen #79254; Qiagen-Germantown MD USA).
2011-12-07 | E-GEOD-25965 | biostudies-arrayexpress