Transcription profiling of 74 kidney tumor samples of different histological type, differentiation grade, stage and with data on chromosomal aberrations and follow-up
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ABSTRACT:
ORGANISM(S): Homo sapiens
SUBMITTER: Wolfgang Huber
PROVIDER: E-DKFZ-1 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Congenital Hypothyroidism occurs in 1:3500 live births and is therefore the most common congenital endocrine disorder. A spectrum of defective thyroid morphology, termed thyroid dysgenesis, represents 80% of permanent CH cases. Although several candidate genes have been implicated in thyroid development, comprehensive screens failed to detect mutation carriers in a significant number of patients with non-syndromic TD. Due to the sporadic occurrence of TD, de novo chromosomal rearrangements are conceivably representing one of the molecular mechanisms participating in its aetiology. Recently, the use of array CGH technique has provided the ability to map these variations genomewide with high resolution. We performed an array CGH screen of 74 TD patients to determine the role of copy number variants (CNV) in the aetiology of the disease. We identified novel CNVs in 8.75% of all patients that have not been described as frequent variations in the healthy population. Affected patients presented with athyreosis or thyroid hypoplasia and in one case with associated heart malformation. We selected 74 patients with thyroid dysgenesis for array CGH analysis. All individuals were detected in neonatal screening programs and abnormal thyroid gland morphology was subsequently confirmed by ultrasound examination. Intragenic mutations in NKX2-1, FOXE1 and NKX2.5 had been previously excluded in phenotype characteristic individuals. PAX8 mutations were excluded in all patients with hypoplastic thyroids by direct sequencing of the coding exons 1-11. The study was approved by the local ethics committee. Genomic DNA of all subjects as well as of healthy controls was isolated from peripheral blood leucocytes using the Qiagen DNA blood mini kit (Qiagen, Hilden, Germany). Array-comparative genomic hybridization was carried as described previously {Erdogan, 2006 #142; Pinkel, 1998 #151}. In brief, sonicated patient- and control DNA was labeled by random priming with Cy3-dUTP and Cy5-dUTP (Bioprime Array CGH, Invitrogen, Carlsbad, CA), respectively, and hybridized onto a submegabase resolution tiling path BAC array, consisting of ~ 36 000 BAC clones obtained from several sources as described elsewhere {Fiegler, 2003 #198; Ishkanian, 2004 #196; Krzywinski, 2004 #197} . Step-by-step protocols are also provided at http://www.molgen.mpg.de/~abt_rop/molecular_cytogenetics/. Arrays were scanned with the G2565BA Agilent Microarray Scanner System (resolution 10 µm; PMT 100 % for Cy3/Cy5, respectively) (Agilent Inc. Santa Clara, CA) and analyzed using GENEPIX Pro 5.0 Software. Analysis and visualization of array CGH data were performed with our software package CGHPRO {Chen, 2005 #143}. For the assessment of copy number gains and losses, we used conservative log2 ratio thresholds of 0.3 and -0.3, respectively. Deviant signal intensity ratios involving three or more consecutive BAC clones were considered to be potentially pathogenic, unless they were covered by more than one known DNA copy number variant, as listed in the Database of Genomic Variants (http://projects.tcag.ca/variation/) or covered by > 50% of their length at least once in our reference set of 600 samples. Potentially pathogenic CNVs were verified by array CGH on a 244k oligonucleotide array from Agilent following the manufacturer’s instructions (Protocol-No. G4410-90010). Confirmed CNVs were tested for inheritance by co-hybridization of parental DNA on BAC arrays as described above. All chromosome coordinates are referring to the UCSC Genome Browser Assembly May 2004 (hg17/ NCBI Build 35; available at: http://genome.ucsc.edu/cgi-bin/hgGateway?hgsid=99195739&clade=vertebrate&org=Human&db=hg17). Cytoscape {Shannon, 2003 #201} was used for the elucidation of potential interactions between genes within the intervals of interest.
2010-05-31 | E-GEOD-18152 | biostudies-arrayexpress
Project description:Congenital Hypothyroidism occurs in 1:3500 live births and is therefore the most common congenital endocrine disorder. A spectrum of defective thyroid morphology, termed thyroid dysgenesis, represents 80% of permanent CH cases. Although several candidate genes have been implicated in thyroid development, comprehensive screens failed to detect mutation carriers in a significant number of patients with non-syndromic TD. Due to the sporadic occurrence of TD, de novo chromosomal rearrangements are conceivably representing one of the molecular mechanisms participating in its aetiology. Recently, the use of array CGH technique has provided the ability to map these variations genomewide with high resolution. We performed an array CGH screen of 74 TD patients to determine the role of copy number variants (CNV) in the aetiology of the disease. We identified novel CNVs in 8.75% of all patients that have not been described as frequent variations in the healthy population. Affected patients presented with athyreosis or thyroid hypoplasia and in one case with associated heart malformation.
2010-06-01 | GSE18152 | GEO
Project description:Oral potentially malignant disorders (OPMDs) characterized by the presence of dysplasia and DNA copy number aberrations (CNAs), may reflect chromosomal instability (CIN) and predispose to oral squamous cell carcinoma (OSCC). Early detection of OPMDs with such characteristics may play a crucial role in OSCC prevention. The aim of this study was to explore the relationship between CNAs, histological diagnosis, oral subsite and aneuploidy in OPMDs/OSCCs. Samples from OPMDs and OSCCs were processed by high-resolution DNA flow cytometry (hr DNA-FCM) to determine the relative nuclear DNA content. Additionally, CNAs were obtained for a subset of these samples by genome-wide array comparative genomic hybridization (aCGH) using DNA extracted from either diploid or aneuploid nuclei suspension sorted by FCM. Our study shows that: i) aneuploidy, global genomic imbalance (measured as the total number of CNAs) and specific focal CNAs occur early in the development of oral cancer and become more frequent at later stages; ii) OPMDs limited to tongue (TNG) mucosa display a higher frequency of aneuploidy compared to OPMDs confined to buccal mucosa (BM) as measured by DNA-FCM; iii) TNG OPMDs/OSCCs show peculiar features of CIN compared to BM OPMDs/OSCCs given the preferential association with total broad and specific focal CNA gains. Follow-up studies are warranted to establish whether the presence of DNA aneuploidy and specific focal or broad CNAs may predict cancer development in non-dysplastic OPMDs.
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Project description:Prostate cancer is one of the most commonly diagnosed cancers among men in the world and the pathogenesis of prostate cancer remains poorly understood. In this study, we intended to disclose chromosomal aberrations that might be involved in tumorigenesis, using cDNA microarray-based CGH technology. Keywords: disease state analysis A total of 18 experiments were performed without replicates, using a kidney tissue as normal references. Prostate tumors and normal references were labeled with Cy5-dCTP and Cy3-dCTP, respectively.
2008-09-25 | E-GEOD-6040 | biostudies-arrayexpress
Project description:Biobanking of tissue from clinically obtained kidney biopsies for later analysis with multi-omic approaches, such as single cell technologies, proteomics, metabolomics and the different types of imaging, is an inevitable step to overcome the need of disease model systems and towards translational medicine. Hence, collection protocols that ensure integration into daily clinical routines by the usage of preservation media that do not require liquid nitrogen but instantly preserve kidney tissue for both clinical and scientific analyses are necessary. Thus, we modified a robust single nucleus dissociation protocol for kidney tissue stored snap frozen or in the preservation media RNAlater and CellCover. Using porcine kidney tissue as surrogate for human kidney tissue, we conducted single nucleus RNA sequencing with the widely recognized Chromium 10X Genomics platform. The resulting datasets from each storage condition were analyzed to identify any potential variations in transcriptomic profiles. Furthermore, we assessed the suitability of the preservation media for additional analysis techniques such as proteomics, metabolomics, and the preservation of tissue architecture for histopathological examination including immunofluorescence staining. In this study, we show that in daily clinical routines the preservation medium RNAlater facilitates the collection of highly preserved kidney biopsies and enables further analysis with cutting-edge techniques like single nucleus RNA sequencing, proteomics and histopathological evaluation. Only metabolome analysis is currently restricted to snap frozen tissue. This work will contribute to build tissue biobanks with well-defined cohorts of the respective kidney disease that can be deeply molecular characterized, opening up new horizons for the identification of unique cells, pathways and biomarkers for the prevention, early identification and targeted therapy of kidney diseases.
2024-07-31 | GSE239442 | GEO
Project description:IntroductionThe objective was to describe the prevalence, types, and predictors of adverse events (AEs) in rheumatoid arthritis (RA) patients treated with infliximab and methotrexate in a daily clinical setting.MethodsThis was a prospective, multi-center, open-label, 74-week observational study in patients with active RA despite treatment with methotrexate and at least one other disease-modifying anti-rheumatic drug. Patients were treated with 3 mg/kg infliximab at weeks 0, 2, and 6 and then every 8 weeks. At weeks 0, 6, 26, 50, and 74, patients answered a health assessment questionnaire, a swollen joint count was made, and adverse events (AEs) occurring during the previous period were registered.ResultsFive hundred and seventy-five patients were treated with infliximab, of which 346 were still on infliximab at the study end, 158 discontinued treatment, and 71 were lost to follow-up. Reasons for discontinuation included safety (n=74), elective reasons (n=43), and inefficacy (n=41). Infusion reactions (n=33) and infections (n=20) were the most common AEs causing discontinuation and the most common AEs overall. There were four cases of tuberculosis, all of which occurred in patients negative at screening. Total AEs, serious AEs, and infusion reactions as well as discontinuations for AEs were most frequent during the first 26 weeks. Higher age was a predictor of serious adverse events (SAEs), infection, and discontinuation due to an SAE, but odds ratios were close to one.ConclusionsAEs and discontinuations due to AEs occur most frequently during the first half year of infliximab treatment in refractory RA patients. The main reasons for discontinuing treatment are infections and infusion reactions. Tuberculosis and other infections remain an important concern in these patients.
| S-EPMC2911915 | biostudies-literature
Project description:Lupus nephritis (LN) is characterized by immune-complex deposition in kidney glomeruli and has been classified according to histological features, but has not been characterized on a molecular level. This study aimed to characterize the relationship between histological and molecular phenotypes in LN. Renal compartmental mRNA expression was measured in 54 kidney biopsy specimens from patients with LN and correlated to histological phenotypes. The top identified transcripts were compared to a separate longitudinal cohort of 36 patients with paired kidney biopsies obtained at the time of flare and at follow up. Unsupervised clustering based on mRNA abundance resulted in clear separation by renal compartment, but did not demonstrate a relationship with LN class based on the International Society of Nephrology/Renal Pathology Society (ISN/RPS) classification, or the NIH activity and chronicity indices. A strong interferon gene signature was observed in both cohorts. FN1, SPP1, and LGALS-3 correlated with disease activity in both cohorts. The relationship between mRNA expression and ISN/RPS classification is modest. However, correlation of mRNA expression with individual histologic lesions identifies transcripts that change with resolution of disease flare, and provide insights into the molecular pathways potentially responsible for pathologic kidney lesions. Combining molecular and pathologic kidney biopsy phenotype may hold promise to better classify disease and identify actionable treatment targets.
2019-10-29 | GSE127797 | GEO
Project description:Changes in gene expression in lymph node and kidney of cattle infected with alcelaphine herpesvirus-1. All animals in the group infected with AlHV-1 showed clinical signs of Malignant catarrhal fever (MCF) within one month. Diagnosis of MCF in these animals was confirmed by diagnostic PCR. No clinical signs were seen in the control animals, which were subject to post-mortem examination separately from the MCF-affected animals. RNA samples from kidney and lymph node of 4 MCF-affected and 4 control animals that passed the RNA quality criteria were used for array analysis. Quality assessments of probe-level Affymetrix chip data and normalised data were carried out using statistical and graphical methods including MA plots and smoothed histogram plots. The MA-plots showed normalisation was effective; while smoothed histograms indicated there was no systematic bias in the data.
2012-10-26 | E-MEXP-3497 | biostudies-arrayexpress
Project description:Hybridization of one kidney of cortisol treated fish vs. one kidney of control fish. Kidneys were collected from untreated juvenile sea bream (n=4) and from fish, which received for 72h a coconut-oil implant containing 10mg/Kg (fish wet weight) (n=4) cortisol. Experiments were carried out at the University of the Algarve, Portugal in accordance with National legislation for the welfare of animals. Experiments were conducted in two 125 l cylindriconical tanks supplied with a continuous through-flow of oxygenated seawater at 20+1 °C using juvenile sea bream (25 g + 3 g) adapted for 1 week to the experimental conditions. One tank contained 8 untreated fish (control) and the other tank 8 cortisol treated fish and the end of experiments fish were removed form tanks, decapitated and the kidneys rapidly removed and place in RNAlater (Qiagen) at â20 °C. No mortality occurred in the control tank but 2 fish died in the cortisol treated tank.
2010-06-11 | E-GEOD-2064 | biostudies-arrayexpress
Project description:IntroductionMultiple primary lung cancers (MPLCs) occur in common carcinogenetic risks such as lifestyle, biological aging, immune responses, hormones, and metabolism. Although MPLCs harbor various genetic profiles within the same individuals, differences in the tumor microenvironment (TME) are unclear. We investigated the impact of genetic aberrations, non-intrinsic factors, and pathological subtypes on tumor immunity.Materials and methodsIn total, 73 surgically resected specimens from 32 patients with MPLC were analyzed. PD-L1 expression in tumor cells (TCs) and immune cells (ICs), CD3-positive tumor-infiltrating lymphocytes (TILs), CD8/CD3 ratios, and FOXP3-positive TILs that compose TMEs were evaluated by immunohistochemistry and classified on a score of 0-2. 38 tumors were sequenced for somatic mutations in 409 cancer-associated genes.ResultsFemales and never or light smokers had a higher incidence of PD-L1-negative tumors and a higher concordance rate. PD-L1 positivity in TCs and ICs was significantly less frequent in EGFR-mutated than in wild-type tumors. Differences in the score of TMEs were observed between the KRAS-mutated-only tumor and the KRAS and TP53-co-mutated tumors, and between the KRAS-mutated-only tumor and the KRAS and STK11-co-mutated tumors. Significantly more FOXP3-high TILs were observed in invasive pathological subtypes than in non-invasive ones.ConclusionComparing TMEs among MPLCs revealed that non-smokers or light smokers and females were unlikely to express PD-L1 regardless of tumor site and confirmed that the EGFR mutations and co-occurring KRAS and STK11 or TP53 mutations were associated with TME. Pathological subtypes may impact the efficacy of immune therapy due to their potential correlations with regulatory T cells.
| S-EPMC8102176 | biostudies-literature