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PLASMA biomarkers of Idiopathic Pulmonary Fibrosis

ABSTRACT: The aim of the current study is to find plasma-based biomarker candidates for Idiopathic Pulmonary Fibrosis (IPF). Incidence of IPF seems to be increasing in Europe and there is significant mortality associated with IPF. There are no sensistive biomarkers for IPF and diagnosis is entirely clinical and/or histopathological which is often delayed. Minimally invasive biomarkers of IPF would be expected to aid clinicians perfrom early diagnosis of IPF enabling better management of the disease.

INSTRUMENT(S): Synapt MS

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma, Blood

SUBMITTER: Sakari Joenväärä

LAB HEAD: Risto Renkonen

PROVIDER: PXD010965 | Pride | 2020-05-13

REPOSITORIES: Pride

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			Action	DRS
	20180124_IPF_Proteomics_01.raw.zip	Raw
	20180124_IPF_Proteomics_02.raw.zip	Raw
	20180124_IPF_Proteomics_03.raw.zip	Raw
	20180124_IPF_Proteomics_04.raw.zip	Raw
	20180124_IPF_Proteomics_05.raw.zip	Raw

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Publications

Label-free plasma proteomics identifies haptoglobin-related protein as candidate marker of idiopathic pulmonary fibrosis and dysregulation of complement and oxidative pathways.

Saraswat Mayank M Joenväärä Sakari S Tohmola Tiialotta T Sutinen Eva E Vartiainen Ville V Koli Katri K Myllärniemi Marjukka M Renkonen Risto R

Scientific reports 20200508 1

Idiopathic pulmonary fibrosis (IPF) is a lung parenchymal disease of unknown cause usually occurring in older adults. It is a chronic and progressive condition with poor prognosis and diagnosis is largely clinical. Currently, there exist few biomarkers that can predict patient outcome or response to therapies. Together with lack of markers, the need for novel markers for the detection and monitoring of IPF, is paramount. We have performed label-free plasma proteomics of thirty six individuals, 1 ...[more]

PMID: 32385381

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MicroRNA expression data from lung tissue of Idiopathic Pulmonary Fibrosis

Project description:Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive, and usually lethal lung disease characterized by unknown causes and few treatment options We used microarray to determine the expression of miRNA and 17 miRNAs were differentially expressed in IPF lungs, including 10 upregulated and 7 downregulated miRNAs. Lung tissue was obtained from 4 IPF patients with histological evidence of usual interstitial pneumonia at the time of surgical lung biopsy or lung transplantation. The diagnosis of IPF was derived according to the standards accepted by the American Thoracic Society/European Respiratory Society. Histological normal lung tissues used as controls was obtained from 3 patients with primary spontaneous pneumothorax at the time of thoracoscopy with stapling of any air leak.The miRNA expression profile was determined by Affymetrix microarray, and transcriptome with Affymetrix array

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Spatial transcriptomics (Visium, 10x Genomics) data for human Idiopathic Pulmonary Fibrosis (IPF) and control lung tissue

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Profiling of Gene Expression in Idiopathic Pulmonary Fibrosis

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Profiling of Gene Expression in Idiopathic Pulmonary Fibrosis

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Serial Analysis of Gene Expression molecular signature for disease progression in Idiopathic Pulmonary Fibrosis

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Peripheral Blood Mononuclear Cell Gene Expression Profiles May Predict Poor Outcome in Idiopathic Pulmonary Fibrosis [Agilent]

Project description:Background: In this study we aimed to identify peripheral blood mononuclear cell (PBMC) gene expression profiles predictive of poor outcomes in idiopathic pulmonary fibrosis (IPF) Methods: Microarray analyses of PBMC were performed in 120 patients from discovery (n=45) and replication cohorts (n=75). Genes and pathways associated with transplant-free survival (TFS) were identified and confirmed by qRT-PCR. Findings: 52 genes were predictive of TFS in a discovery cohort (FDR<5%, Cox score above 2.5 or below -2.5). Clustering the replication cohort samples using these genes distinguished two patient groups with significantly different TFS (hazard ratio 1.96, 95%CI 1.01-3.8, P=0.018). Decreased expression of M-bM-^@M-^\The co-stimulatory signaling during T cell activationM-bM-^@M-^] Biocarta pathway and in particular CD28, ICOS, LCK and ITK was associated with shorter TFS times in each cohort (FDR<5%). qRT-PCR expression of CD28, ICOS, LCK and ITK correlated with the microarray results in the discovery cohort (P<0.05) and their decreased expression was predictive of shorter TFS in the replication cohort (P<0.05). A genomic and clinical model demonstrated an area under the ROC curve of 78.5% at 2.4 months for death and lung transplant prediction. Interpretation: Our results suggest that CD28, ICOS, LCK and ITK are outcome biomarkers in IPF. PBMC from 75 patients with the diagnosis of IPF were obtained within 30 minutes from blood draw. Total RNA was extracted, labeled and hybridized to Agilent Whole Human Genome Oligo Microarray, 4 x 44K. Patients were followed from blood draw until death, transplant or last follow up. Hierarchical clustering and gene-set analysis with censored outcome data were used to study the association of gene expression and outcome in this cohort (replication cohort)

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