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.

Project description:In normal skin, interactions between melanocytes and keratinocytes, and between melanocytes and the basal membrane are functionally relevant for maintenance of homeostasis and epidermal melanin unit whose deregulation may trigger a continuous proliferation of the melanocytes. In order to further elucidate the molecular events related to cell-cell and cell-ECM interactions in relation to the biology of melanomas, we analyzed the expression profile of 64 human melanomas, 21 primary samples and 43 independent metastasis. Tissue samples melanomas were obtained at Hospital A. C. Camargo. All patients signed an informed consent and the study was approved by our internal ethics committee. Tissue samples obtained by surgery were snap-frozen in liquid nitrogen and biopsy samples were collected in RNAlaterTM (Ambion, Austin, TX). Non-tumor areas were removed by handy dissection and only samples represented by at least 70% of tumors cells within their natural stroma were selected for RNA extraction. Total RNA was extracted using RNeasy Midi-Kit® and amplified by a T7-based protocol. An indirect cDNA-labeling was performed as described by Cox et al. (2004). We used dual-label system in which two RNA samples (test and reference) were separately reverse-transcribed, labeled, mixed, and hybridized together to each array. Each sample was hybridized in duplicate, with dye swap between sample and reference. As reference RNA we used a pool of equal amounts of total RNA from 5 human cutaneous melanoma cell lines (SK-MEL 05; 17; 28; 37 and 188, kindly provided by Dr. Alan Houghton, MSKCC, New York, NY, USA). We used glass arrays containing 4.800 cDNA sequences (Brentani et al. 2003) were prepared in our lab with the aid of the Flexys robot17 (Genomic Solutions, Cambridgeshire, United Kingdom). The list of immobilized genes can be obtained at GEO, accession number GPL1930. Pre-hybridization, hybridization and washing were performed as previously described (Gomes et al. 2003; 2005), and slides were scanned on a laser scanner (ScanArray Express, PerkinElmer Life Sciences, Boston, MA). Data were extracted with ScanArray Express software (PerkinElmer Life Sciences, Boston, MA) using the histogram method.

Project description:To obtain insight into the molecular basis of ductal carcinoma in situ (DCIS) and its progression by infiltrating surrounding tissue, we have performed cellular-based gene expression analysis of pure DCIS and DCIS with co-existing invasive ductal carcinoma (IDC) and compared the histological and molecular aspects between these morphologically identical lesions seeking to find key genes involved in DCIS progression. For that, 30 samples were evaluated, 4 non-neoplastic (N), 5 pure DCIS, 11 DCIS with co-existing IDC (DCIS-IDC) and 10 IDC. All samples were laser capture microdissected and RNAs were amplified using T7-based methodology. Microarray technology was performed using a customized cDNA platform containing 4,608 human genes. To classify the 4 sample groups according to molecular similarity we performed comparisons of their general expression pattern using ANOVA test (pFDR<0,01) followed by Tukey´s test (fold>l2l). Among the 4 sample groups, as expected, non-neoplastic cells reported the most distinct gene expression pattern. However, among the 3 groups of neoplastic cells, in contrast to morphological aspects, pure DCIS had the most distinct expression profile when compared to the other lesions: DCIS-IDC and IDC. Additionally, by comparison among pure DCIS, DCIS-IDC and N, we identified 147 genes potentially involved in DCIS progression. Unsupervised hierarchical cluster based on expression profile of this gene-set could discriminate DCIS-IDC from 60% of pure DCIS samples. Keywords: disease state analysis Fresh-frozen human breast samples were retrieved from the Tumor Tissue Biobank of the Medical and Research Center - Hospital A. C. Camargo, São Paulo. This research was approved by Ethic Committee of the Medical and Research Center - Hospital A. C. Camargo under number 587/04 and a written informed consent signed by all participants. All patients had presented at least 5 years of follow-up. Thirty samples were evaluated, 4 non-neoplastic breast samples (MN), 5 pure DCIS (stage 0; DCIS-0), 11 DCIS with co-existing IDC (DCIS) and 10 IDC. The non-neoplastic samples were obtained from perilesional mammary specimens from patients submitted to resection of benign lesions. All cells types were laser capture microdissected using PixCell II LCM system (Arcturus Engineering, Mountain View, CA). The total RNA was extracted by using the PicoPureä RNA Isolation kit (Arcturus Engineering # KT0204). A two-round linear amplification procedure based on T7-driven amplification was carried out. Amplified RNA was then used in a transcriptase reverse reaction into cDNA in the presence of Cy3- or Cy5-labeled dCTP. HB4a normal luminal epithelial mammary cell line (O’Hare et al 1991) was amplified following the same protocol and used as reference for microarray hybridizations. Dye swap was performed for each sample analyzed and used as replicate samples. For the raw_data (lowess_data), see Web Link below.

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.

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).

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.

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Gene expression profile of HNSCC

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