Biopsy proteome scoring to determine mucosal remodeling in celiac disease
Ontology highlight
ABSTRACT:
INSTRUMENT(S): Q Exactive HF
ORGANISM(S): Homo Sapiens (human)
SUBMITTER: 
Anette Johansen
LAB HEAD: Jorunn Stamnæs
PROVIDER: PXD045913 | Pride | 2024-03-15
REPOSITORIES: Pride
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| 1a-4b.zip | Other | |||
| A1Anette.raw | Raw | |||
| A1Anette_220608022510.raw | Raw | |||
| A2Anette.raw | Raw | |||
| A2Anette_220608045028.raw | Raw |
Items per page: 5 1 - 5 of 165 |
Similar Datasets
Project description:Molecular and genomic analysis of microscopic quantities of tumor from formalin-fixed and paraffin-embedded (FFPE) biopsies has many unique challenges. Here we evaluated the feasibility of obtaining transcriptome-wide RNA expression to measure prognostic classifiers from diagnostic prostate needle core biopsies. 158 samples from diagnostic needle core biopsies (Bx) and radical prostatectomies (RP) were collected from 33 patients at three hospitals, each patient provided up to 6 tumor and benign samples. Genome-wide transcriptomic profiles were generated using Affymetrix Human Exon arrays for comparison of gene expression alterations and prognostic signatures between the Bx and RP samples. For 23 patients from UCSF and CSMC, six prostate tissue samples were obtained from each patient: tumor biopsy, tumor RP, benign adjacent biopsy, benign adjacent RP, and benign contralateral biopsy, and benign contralateral RP. For the 10 UHN patients only tumor biopsy and tumor RP samples were obtained. A total of 147 samples passed RNA, cDNA, and microarray quality control.
2016-03-09 | E-GEOD-72220 | biostudies-arrayexpress
Project description:Renal cell cancer is among the most common forms of cancer in humans, with around 35,000 deaths attributed to kidney carcinoma in the European Union (EU) in 2012 alone. Clear cell renal cell carcinoma (ccRCC) represents the most common form of kidney cancer and the most lethal of all genitourinary cancers. Here we apply omics technologies to archival core biopsies to investigate the biology underlying ccRCC. Knowledge of these underlying processes should be useful for the discovery and/or confirmation of novel therapeutic approaches and ccRCC biomarker development. From partial or full nephrectomies of 11 patients, paired core biopsies of ccRCC affected tissue and adjacent non-tumorous tissue were both sampled and subjected to proteomics analyses. We combined proteomics results with our published mRNA-seq from the same patients and with published miRNA-seq data from an overlapping patient cohort from our institution. Statistical analysis and pathway analysis were performed with JMP Genomics (SAS) and Ingenuity Pathway Analysis (IPA, Qiagen), respectively. Proteomics analysis confirmed the involvement of metabolism and oxidative stress-related pathways in ccRCC, while the most affected pathways in the mRNA-seq data were related to the immune system. Unlike proteomics or mRNA-seq alone, a combinatorial cross-omics pathway analysis approach captured a broad spectrum of biological processes underlying ccRCC, such as mitochondrial damage, repression of apoptosis, and immune system pathways. Sirtuins, immunoproteasome genes and CD74 are proposed as potential targets for the treatment of ccRCC.
2019-04-25 | PXD011681 | Pride
Project description:Analysis of intra- and inter variation using multiple biopsies taken from the same knee. The biopsies were obtained from thirteen different patients; seven by orthopedic surgery and six by rheumatic arthroscopy. Orthopedic samples (patients 1-7 Three synovial tissue specimens were obtained from random sites of the synovium for each patient. Biopsy III of patient 7 was not used due to bad RNA quality. For patients 1-3 each biopsy was divided into three parts (1/3 of a biopsy is denoted subbiopsy). In total this resulted in 39 specimens from the orthopedic patients (nine biopsies from patients 1-3 and three biopsies from each of patients 4-7). For patient 1-3, pt1 b1.BA means patient 1 biopsy 1 subbiopsy B Technical replicate A. For patient 4-7, pt4 b1A means patient 4 biopsy 1 technical replicate A. Arthroscopic samples (patients 8-13) Arthroscopic biopsies were taken at the site of inflammation close to cartilage (cc) or not close to cartilage (ncc), defined as less or more than 1.5 cm away from cartilage, respectively. Multiple biopsies were taken from two sites in patients 8, 11, 12, 13 and from four sites in patients 9 and 10. pt12_ncc_1A means patient 12 not close to cartilage biopsy 1 technical replicate.
2005-06-22 | E-MEXP-367 | biostudies-arrayexpress
Project description:Background: Multiple autoantigens have been identified in membranous nephropathy (MN) by tissue-based proteomics. However, the antigenic targets of disease are unknown for >10% of MN and >50% of membranous lupus nephritis (MLN) cases. We identified multiple new targets in PLA2R-/THSD7A-/EXT-/NELL1-quadruple negative MN biopsies through mass spectrometry (MS) of immune complexes recovered from biopsy tissue of patients with MN. Methods: MN cases negative for PLA2R, THSD7A, EXT1/2, and NELL1 were identified from a biopsy database. Protein G immunoprecipitation was used to recover immune complexes from frozen biopsy tissue, followed by interrogation by mass spectrometry (MS). Potential antigens were confirmed through paraffin immunofluorescence of protein targets, followed by co-localization with IgG within immune deposits. Consecutive series of 165 cases of PLA2R-negative MN biopsies and 95 MLN biopsies was screened to determine the frequency for each potential antigen. Results: Seven protein targets were discovered within immune complexes from MN biopsies including FCN3, CD206, EEA1, SEZ6L2, NPR3, MST1, and VASN. Peptides from these proteins on MS were not enriched in PLA2R (n=86), THSD7A (n=64), NELL1 (n=64), or EXT1/2 (n=60) controls. Between 3-30 unique peptides were detected for each target. Frequencies of each antigen, determined by staining consecutive case series, were SEZ6L2 (1/165 idiopathic; 0/95 MLN), VASN (8/165 idiopathic; 2/95 MLN), EEA1 (6/165 idiopathic; 7/95 MLN), MST1 (6/165 idiopathic; 2/95 MLN), and FCN3 (0/165 idiopathic, 6/95 MLN), NPR3 and CD206 were positive in index cases. All cases showed co-localization of IgG within immune deposits. Conclusion: Seven novel protein targets were identified in MN and MLN.
2023-04-06 | PXD035854 | Pride
Project description:This study describes a comparison of global proteome expression in small intestinal tissue collected from celiac disease patients at different stages of disease. We have analyzed sections from FFPE biopsy blocks and identified more than 4500 protein without sample pre-fractionation. We have compared protein expression in two sample cohorts that were chosen retrospectively from patients participating in research protocols at our facility. First we compared biopsies from 10 patients collected at the time of diagnoses (untreated CD) with biopsies collected 1 year later following gluten free diet (treated CD). We observed overall good agreement between differential expression of proteins and histological changes that occur in the intestine. We identified biological pathways that are known to operate in the disease lesion. We also observed a strong signal for neutrophil infiltration. By use of a dedicated immunoglobulin variable gene family database we found that differential expression of IGHV5-51 distinguished our untreated from treated CD patients. We also compared protein expression in 4 treated CD patients that developed histological changes in the small intestine in response to a 3 day gluten challenge. Although these patients develop an intestinal lesion resembling the lesion observed in untreated patients, we observed differential expression of proteins involved in acute tissue remodeling that were not seen when we compared UCD to TCD samples. Our study presents a proof-of-concept to demonstrate that analysis of material from FFPE tissue block material can provide a comprehensive overview of many disease processes that occur in the celiac small intestine. Changes in protein expression will reveal information on disease state that may not be observed by histological evaluation
2018-11-21 | PXD008992 | Pride
Project description:Background: Multiple autoantigens have been identified in membranous nephropathy (MN) by tissue-based proteomics. However, the antigenic targets of disease are unknown for >10% of MN and >50% of membranous lupus nephritis (MLN) cases. We identified multiple new targets in PLA2R-/THSD7A-/EXT-/NELL1-quadruple negative MN biopsies through mass spectrometry (MS) of immune complexes recovered from biopsy tissue of patients with MN. Methods: MN cases negative for PLA2R, THSD7A, EXT1/2, and NELL1 were identified from a biopsy database. Protein G immunoprecipitation was used to recover immune complexes from frozen biopsy tissue, followed by interrogation by mass spectrometry (MS). Potential antigens were confirmed through paraffin immunofluorescence of protein targets, followed by co-localization with IgG within immune deposits. Consecutive series of 165 cases of PLA2R-negative MN biopsies and 95 MLN biopsies was screened to determine the frequency for each potential antigen. Results: Seven protein targets were discovered within immune complexes from MN biopsies including FCN3, CD206, EEA1, SEZ6L2, NPR3, MST1, and VASN. Peptides from these proteins on MS were not enriched in PLA2R (n=86), THSD7A (n=64), NELL1 (n=64), or EXT1/2 (n=60) controls. Between 3-30 unique peptides were detected for each target. Frequencies of each antigen, determined by staining consecutive case series, were SEZ6L2 (1/165 idiopathic; 0/95 MLN), VASN (8/165 idiopathic; 2/95 MLN), EEA1 (6/165 idiopathic; 7/95 MLN), MST1 (6/165 idiopathic; 2/95 MLN), and FCN3 (0/165 idiopathic, 6/95 MLN), NPR3 and CD206 were positive in index cases. All cases showed co-localization of IgG within immune deposits. Conclusion: Seven novel protein targets were identified in MN and MLN.
2023-04-06 | PXD035853 | Pride
Project description:The presence of Donor-Specific anti-HLA Antibodies (DSA) is associated with an increased risk of both acute and chronic antibody-mediated rejection (AMR) in kidney allografts. AMR has remained challenging in kidney transplantation and is the major cause of late allograft loss. However, not all patients with DSA develop AMR, leading to the question of whether this represents accommodation, if other protective mechanisms exist or if this is actually a state of pre-rejection. Clinical and histological features, and gene expression profiles of kidney biopsy and blood samples of donor-specific antibody (DSA)+ patients without rejection were compared to antibody-mediated rejection (AMR) patients to elucidate the mechanisms involved in prevention of AMR. Of the 71 DSA+ patients, 46 had diagnosis of AMR and 25 did not show rejection. 50 DSA- patients without rejection were used as control. A subgroup of patients with available biopsy (n=61) and blood samples (n=54) were analyzed by microarrays. Both, DSA+/AMR+ and DSA+/AMR- biopsies showed increased expression of gene transcripts associated with cytotoxic T, natural killer cells, macrophages, interferon-gamma and rejection compared to DSA- biopsies. Regulatory T cell transcripts were up-regulated in DSA+/AMR+ and B cell transcripts in DSA+/AMR- biopsies. Whole blood gene expression analysis showed increased immune activity in only DSA+/AMR+ patients. There were no differentially expressed tolerant genes studied (n=14) in the blood or biopsy specimens of DSA+/AMR- patients. During a median 36 months follow-up, 4 DSA+/AMR- patients developed AMR, 12 continued to have DSAs but 9 lost DSAs. Gene expression profiles did not predict the development of AMR or persistence of DSAs. These results indicate increased immune activity in DSA+/AMR- biopsies despite lack of histologic findings of rejection. All clinically indicated kidney transplant biopsies performed at our institution after January 2009 were reviewed and 263 patients with anti-HLA antibody testing at the time of biopsy were identified. There were 71 DSA+ and 192 DSA- patients (Figure 1). Of the 71 DSA+ patients, 46 had biopsy diagnosis of acute AMR (n=9) or chronic AMR (n=37), and 25 had normal histopathology or minimal non-specific interstitial fibrosis/tubular atrophy (IFTA). Of the 192 DSA- patients, 50 patients with normal histology and/or mild non-specific IFTA were used as a control group. Clinical and histopathological findings of these 3 groups (DSA+/AMR+, DSA+/AMR- and DSA-) were analyzed. A subgroup of patients who were enrolled in the Institutional Review Board-approved âImmune Monitoring Studyâ who had clinically indicated biopsy (n=61) and whole blood samples (n=54) stored were used for genomic analysis. Twenty-eight biopsy and blood samples from DSA+/AMR+ patients, 13 biopsy and 14 blood samples from DSA+/AMR- patients, and 20 biopsy and 12 blood samples from DSA- patients, were available for microarray analysis.
2013-08-23 | E-GEOD-50084 | biostudies-arrayexpress
Project description:The purpose of this experiment was to do investigatge the transcriptional effect of anti-TNF treatment in patients suffering from rheumatoid arthritis. Two series of hybridizations were performed. Each hybridization was done with a technical replicate (the same amount of RNA taken from the same amplified RNA aliquot labeled in two separate reactions and hybridized onto two separate arrays). In the first series of hybridizations RNA exptracted from biopsies taken before treatment was hybridized in a common reference design to enable comparisons between patients. In the second series RNA from biopsies taken after and before treatment were hybridized on the same chip in a direct design to enable investigation of the effect of treatment. 10 patients (8 females and 2 males, median age 54, range 25-69) meeting the American College of Rheumatology (ACR) criteria for RA were recruited for this study. All patients received infliximab (an antibody directed against TNF-alpha) infusions 3mg/kg at week 0 and than after 2 weeks and 6 weeks. Five of these patients were receiving prednisolon and all ten patients were treated with methotrexate to a maximum of 20 mg per week. Synovial biopsies were obtained during arthroscopy from all patients before and after a median of 9 weeks of treatment (with one exception, patient 7 where the second biopsy was obtained during open surgery). Biopsies were taken at the site of inflammation close to cartilage (cc) or not close to cartilage (ncc), defined as less or more than 1.5 cm away from cartilage, respectively. One biopsy was taken before and after treatment from patient 5, 7, 9 and 10. Multiple biopsies were retrieved before and/or after treatment from patient 1, 2, 3, 4, 6 and 7. Due to small amounts of RNA available for patient 9 it was only used in the second series of hybridizations. The average biopsy weight was 22 mg. The ethical committee at the Karolinska Hospital approved all experiments on human cells and tissues. Informed consent was obtained from all study subjects.
2006-06-16 | E-TABM-104 | biostudies-arrayexpress
Project description:Background: Primary graft dysfunction (PGD) remains a challenge to lung transplantation (LTx) recipients as a leading cause of poor early outcomes. New methods are needed for the rapid detection of PGD and the measurement of particle flow rate (PFR) from exhaled breath is a novel means to monitor disease. Methods: 22 recipient pigs underwent orthotopic left LTx and were evaluated for PGD on the third post-operative day. Exhaled breath particles (EBPs) and PFR were measured on mechanical ventilation. EBPs were evaluated with mass spectrometry and the proteome was compared to tissue biopsies and bronchoalveolar lavage fluid (BALF). Findings were confirmed in EBPs from 11 human transplant recipients. Results: 9 recipients developed PGD and had significantly higher PFR (686.4 (449.7-8824.0) particles per minute (ppm)) compared to recipients without PGD (116.6 (79.7-307.4) ppm, p=0.0005). From proteomic analysis, porcine and human EBP proteins recapitulated the BAL and adherens and tight junction proteins were underexpressed in PGD tissue. Conclusions: Histological and proteomic analysis found significant changes to the alveolar-capillary barrier to explain the increased PFR in recipients with PGD. Combined with the similarity of proteomic profiles between EBPs and BALF, exhaled breath measurement is proposed as a rapid and non-invasive bedside measurement of PGD.
2024-04-05 | PXD046365 | Pride
Project description:Lichtenberg figures (LF), also known as a ferning pattern or keraunographic marking, is a pathognomonic skin sign for a lightning strike injury. The true pathophysiology of LF remains unknown. This dataset describes a case of LF following a high voltage electrical injury in which a skin biopsy was taken directly from the LF.
2021-05-28 | PXD011532 | Pride