Transcriptome Profiles of the Circulating Extracellular Vesicles in Acute Lung Allograft Rejection

Research output: Contribution to journalConference articleScientificpeer-review

Abstract

Summary of Objectives The potential of Extracellular Vesicles (EVs) as novel diagnostic, prognostic and predictive biomarkers in transplantation has been noticed as they are known to contain various molecules related to cell-cell communication that vary depending on the EV's origin, such as DNA, RNA and miRNA, and their ability to deliver these molecules to target cells. Given this factor, we hypothesize that circulating EV from patients may contain transcriptomes derived from host immune cells and allograft endothelium, epithelium, and parenchymal cells that regulate the gene expression related to the development of acute rejection and chronic lung allograft dysfunction. Therefore, we will investigate the circulating EVs' transcriptome by next generation sequencing analysis and compare these results with clinical findings and transcriptomics from transbronchial biopsies to discover novel molecular mechanisms and to develop liquid biopsies for acute rejection in a prospective study. Methods We have collected the recipient's and donor's plasma and transbronchial biopsies. The samples are taken at the time of organ procurement from the donor, and at the time of transplantation, 1 week, 1, 3, and 6 months, and 1 year after lung transplantation and every time when there is clinical suspicion of acute rejection. For this preliminary study, four rejection patients proven with the ISHLT grading system and one patient with suspected acute rejection were randomly chosen. All samples from the five patients and their donors were processed to obtain plasma-derived EVs (n=39). EVs were isolated with ExoRNeasy kit (Qiagen) and the whole transcriptome sequencing was performed to obtain at least 15m pair-ended reads by Illumina HiSeq2000. The sequenced data will be processed further with a bioinformatics pipeline for a downstream analysis to observe differential expression patterns, alternative splicing events, and the discovery of biomarkers. Endpoints We were able to validate the morphology and size distribution of EVs isolated from plasma by electron microscopy and nanoparticle tracking analysis. Since the data are currently in the sequencing data analysis pipeline, we expect the results of this preliminary study to be finished by December 2018. If successful, we will confirm the results with a larger cohort.
Original languageEnglish
JournalJournal of Heart and Lung Transplantation
Volume38
Issue number4, Supplement
Pages (from-to)S146
ISSN1053-2498
DOIs
Publication statusPublished - Apr 2019
MoE publication typeA4 Article in conference proceedings

Cite this

@article{78e974126b1648b28ccf40ddec5e7acf,
title = "Transcriptome Profiles of the Circulating Extracellular Vesicles in Acute Lung Allograft Rejection",
abstract = "Summary of Objectives The potential of Extracellular Vesicles (EVs) as novel diagnostic, prognostic and predictive biomarkers in transplantation has been noticed as they are known to contain various molecules related to cell-cell communication that vary depending on the EV's origin, such as DNA, RNA and miRNA, and their ability to deliver these molecules to target cells. Given this factor, we hypothesize that circulating EV from patients may contain transcriptomes derived from host immune cells and allograft endothelium, epithelium, and parenchymal cells that regulate the gene expression related to the development of acute rejection and chronic lung allograft dysfunction. Therefore, we will investigate the circulating EVs' transcriptome by next generation sequencing analysis and compare these results with clinical findings and transcriptomics from transbronchial biopsies to discover novel molecular mechanisms and to develop liquid biopsies for acute rejection in a prospective study. Methods We have collected the recipient's and donor's plasma and transbronchial biopsies. The samples are taken at the time of organ procurement from the donor, and at the time of transplantation, 1 week, 1, 3, and 6 months, and 1 year after lung transplantation and every time when there is clinical suspicion of acute rejection. For this preliminary study, four rejection patients proven with the ISHLT grading system and one patient with suspected acute rejection were randomly chosen. All samples from the five patients and their donors were processed to obtain plasma-derived EVs (n=39). EVs were isolated with ExoRNeasy kit (Qiagen) and the whole transcriptome sequencing was performed to obtain at least 15m pair-ended reads by Illumina HiSeq2000. The sequenced data will be processed further with a bioinformatics pipeline for a downstream analysis to observe differential expression patterns, alternative splicing events, and the discovery of biomarkers. Endpoints We were able to validate the morphology and size distribution of EVs isolated from plasma by electron microscopy and nanoparticle tracking analysis. Since the data are currently in the sequencing data analysis pipeline, we expect the results of this preliminary study to be finished by December 2018. If successful, we will confirm the results with a larger cohort.",
author = "S. Joo and M. Puhka and R. Krebs and P. Mattila and M. Kankainen and K. Dhaygude and E. Rouvinen and K. Lemstr{\"o}m",
year = "2019",
month = "4",
doi = "10.1016/j.healun.2019.01.348",
language = "English",
volume = "38",
pages = "S146",
journal = "Journal of Heart and Lung Transplantation",
issn = "1053-2498",
publisher = "EXCERPTA MEDICA INC-ELSEVIER SCIENCE INC",
number = "4, Supplement",

}

Transcriptome Profiles of the Circulating Extracellular Vesicles in Acute Lung Allograft Rejection. / Joo, S.; Puhka, M.; Krebs, R.; Mattila, P.; Kankainen, M.; Dhaygude, K.; Rouvinen, E.; Lemström, K.

In: Journal of Heart and Lung Transplantation, Vol. 38, No. 4, Supplement, 04.2019, p. S146.

Research output: Contribution to journalConference articleScientificpeer-review

TY - JOUR

T1 - Transcriptome Profiles of the Circulating Extracellular Vesicles in Acute Lung Allograft Rejection

AU - Joo, S.

AU - Puhka, M.

AU - Krebs, R.

AU - Mattila, P.

AU - Kankainen, M.

AU - Dhaygude, K.

AU - Rouvinen, E.

AU - Lemström, K.

PY - 2019/4

Y1 - 2019/4

N2 - Summary of Objectives The potential of Extracellular Vesicles (EVs) as novel diagnostic, prognostic and predictive biomarkers in transplantation has been noticed as they are known to contain various molecules related to cell-cell communication that vary depending on the EV's origin, such as DNA, RNA and miRNA, and their ability to deliver these molecules to target cells. Given this factor, we hypothesize that circulating EV from patients may contain transcriptomes derived from host immune cells and allograft endothelium, epithelium, and parenchymal cells that regulate the gene expression related to the development of acute rejection and chronic lung allograft dysfunction. Therefore, we will investigate the circulating EVs' transcriptome by next generation sequencing analysis and compare these results with clinical findings and transcriptomics from transbronchial biopsies to discover novel molecular mechanisms and to develop liquid biopsies for acute rejection in a prospective study. Methods We have collected the recipient's and donor's plasma and transbronchial biopsies. The samples are taken at the time of organ procurement from the donor, and at the time of transplantation, 1 week, 1, 3, and 6 months, and 1 year after lung transplantation and every time when there is clinical suspicion of acute rejection. For this preliminary study, four rejection patients proven with the ISHLT grading system and one patient with suspected acute rejection were randomly chosen. All samples from the five patients and their donors were processed to obtain plasma-derived EVs (n=39). EVs were isolated with ExoRNeasy kit (Qiagen) and the whole transcriptome sequencing was performed to obtain at least 15m pair-ended reads by Illumina HiSeq2000. The sequenced data will be processed further with a bioinformatics pipeline for a downstream analysis to observe differential expression patterns, alternative splicing events, and the discovery of biomarkers. Endpoints We were able to validate the morphology and size distribution of EVs isolated from plasma by electron microscopy and nanoparticle tracking analysis. Since the data are currently in the sequencing data analysis pipeline, we expect the results of this preliminary study to be finished by December 2018. If successful, we will confirm the results with a larger cohort.

AB - Summary of Objectives The potential of Extracellular Vesicles (EVs) as novel diagnostic, prognostic and predictive biomarkers in transplantation has been noticed as they are known to contain various molecules related to cell-cell communication that vary depending on the EV's origin, such as DNA, RNA and miRNA, and their ability to deliver these molecules to target cells. Given this factor, we hypothesize that circulating EV from patients may contain transcriptomes derived from host immune cells and allograft endothelium, epithelium, and parenchymal cells that regulate the gene expression related to the development of acute rejection and chronic lung allograft dysfunction. Therefore, we will investigate the circulating EVs' transcriptome by next generation sequencing analysis and compare these results with clinical findings and transcriptomics from transbronchial biopsies to discover novel molecular mechanisms and to develop liquid biopsies for acute rejection in a prospective study. Methods We have collected the recipient's and donor's plasma and transbronchial biopsies. The samples are taken at the time of organ procurement from the donor, and at the time of transplantation, 1 week, 1, 3, and 6 months, and 1 year after lung transplantation and every time when there is clinical suspicion of acute rejection. For this preliminary study, four rejection patients proven with the ISHLT grading system and one patient with suspected acute rejection were randomly chosen. All samples from the five patients and their donors were processed to obtain plasma-derived EVs (n=39). EVs were isolated with ExoRNeasy kit (Qiagen) and the whole transcriptome sequencing was performed to obtain at least 15m pair-ended reads by Illumina HiSeq2000. The sequenced data will be processed further with a bioinformatics pipeline for a downstream analysis to observe differential expression patterns, alternative splicing events, and the discovery of biomarkers. Endpoints We were able to validate the morphology and size distribution of EVs isolated from plasma by electron microscopy and nanoparticle tracking analysis. Since the data are currently in the sequencing data analysis pipeline, we expect the results of this preliminary study to be finished by December 2018. If successful, we will confirm the results with a larger cohort.

U2 - 10.1016/j.healun.2019.01.348

DO - 10.1016/j.healun.2019.01.348

M3 - Conference article

VL - 38

SP - S146

JO - Journal of Heart and Lung Transplantation

JF - Journal of Heart and Lung Transplantation

SN - 1053-2498

IS - 4, Supplement

ER -