The volatile metabolome and microbiome in pulmonary and gastro-intestinal disease - Front matter

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The volatile metabolome and microbiome in pulmonary and gastro-intestinal

disease

van der Schee, M.P.C.

Publication date

2015

Document Version

Final published version

Link to publication

Citation for published version (APA):

van der Schee, M. P. C. (2015). The volatile metabolome and microbiome in pulmonary and

gastro-intestinal disease.

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The volatile metabolome and microbiome in

pulmonary and gastro-intestinal disease

Omics techniques for disease diagnosis,

phenotyping and prognosis.

Marc P van der Schee

Marc P van der Schee

The v

olatile metabolome and micr

obiome in pulmonar

y and gastr

o-intestinal disease

Omics techniques for disease diagnosis, phenotyping and pr

The volatile metabolome and microbiome in

pulmonary and gastro-intestinal disease

The printing of this thesis has generously been supported by a gift from

Cover design : Marijke Fransen - marijkefransen@gmail.com Lay-out : Marijke Fransen - marijkefransen@gmail.com Printed by: www.PRINTERPRO.nl

Copyright © 2015 M.P. van der Schee. All rights reserved. No part of this publication may be reproduced or transmitted in any form or by ane means without prior permission of the author and the publishers of the included scientific papers.

The volatile metabolome and microbiome in

pulmonary and gastro-intestinal disease

ACADEMISCH PROEFSCHRIFT

ter verkrijging van de graad van doctor aan de Universiteit van Amsterdam

op gezag van de Rector Magnificus prof. dr. D.C. van den Boom

ten overstaan van een door het College voor Promoties ingestelde commissie, in het openbaar te verdedigen in de Agnietenkapel

op woensdag 28 januari 2015, te 14:00 uur door Marc Philippe Camille van der Schee

Promotiecommissie

Promotores

Prof. dr. P.J. Sterk

Prof. dr. W.M.C. van Aalderen

Co-promotores

Dr. E.G. Haarman Dr. A.B. Sprikkelman

Overige leden

Prof. dr. A.H. Zwinderman Prof. dr. A.G.J.M. van Leeuwen Prof. dr. J.B. van Goudoever Prof. dr. P.H.M. Savelkoul Dr. M.W.H. Pijnenburg Prof. dr. D.R. Taylor Prof. dr. U. Frey

Paranimfen

Drs. Tim de Meij Drs. Tamara Paff

Propositions

Exhaled volatiles differ between pre-school children with and without respiratory wheeze. After resolution of symptoms this is sustained in children at high risk to develop asthma –

This thesis ∞

Children at increased risk to develop asthma displayed increased microbial abundance and decreased microbial diversity in their nasopharynx compared to controls – This thesis Investing in longitudinal studies in the pediatric population is of prime importance to farther

medical science, as the roots for health and disease are often laid down in the first years of life – this thesis

∞

He who feels knowledge is expensive, doesn’t know the cost of stupidity nor the consequences of ignorance – Alexander Rinooy Kan

Our understanding of health and disease may be greatly enhanced by omics technologies, culminating in personalized health interventions with unprecedented health benefits – This thesis

∞

Prediction is very hard, especially if it’s about the future – Niels Bohr Omics techniques might help us to start thinking about each human as an

individual and unique phenotype – this thesis ∞

We are all too busy to spend any time thinking. But we should – Steven D Levitt A probabilistic approach to the discrimination of disease phenotypes without detailed knowledge of the driving processes holds intrinsic value for clinical medicine – this thesis

∞

We still do not know one thousand of one percent of what nature has revealed to us – Albert E Einstein

We have only began to grasp the potential applications of volatile metabolomics and the considerable challenges to overcome prior to its implementation – this thesis

∞

We are in dire need of that VOC-mentality – Jan Peter Balkenende

It’s time to remove the artificial boundary between clinical and research data to complement evidence based practice with practice based evidence – this thesis

∞

Part I

Introduction

Omics Research in Medicine 3

Not published

Part II

Disease Diagnosis

Electronic Nose Technology for Detection of Invasive 21 Pulmonary Aspergillosis in Prolonged Chemotherapy

Induced Neutropenia: a Proof-of-Principle Study

Journal of Clinical Microbiology (2013), 51(5): 1490-95

Chapter 3

An Electronic Nose Distinguishes Exhaled Breath of 37 Patients with Malignant Pleural Mesothelioma from Controls

Lung Cancer 75 (2012),75(3): 326–331

Chapter 4

The Scent of Cancer 53

Annals of Internal Medicine (2010), 153(11): 766-67

Part III

Disease phenotyping and monitoring

Predicting Steroid Responsiveness in Patients with 59 Asthma Using Exhaled Breath Profiling

Clinical and Experimental Allergy (2013), 43: 1217-25

Chapter 6

Exhaled Molecular Profiles in the Assessment of Cystic 77 Fibrosis and Primary Ciliary Dyskinesia

Journal of Cystic Fibrosis 12 (2013), 12: 454–460

Chapter 7

Faecal Gas Analysis by Electronic Nose as a Novel, 91 Non-invasive Method for Assessment of Active and

Quiescent Paediatric Inflammatory Bowel Disease: Proof of Principle Study

Journal of Chrohn’s and colitis (2014), accepted for publication.

Part IV

Disease prognosis

Altered Exhaled Biomarker Profiles in Children 111 During and After Rhinovirus-induced Wheeze

European Respiratory Journal (2014), accepted for publication

Chapter 9

Increased Microbial Abundance and Decreased 129 Diversity in Preschool Children at Risk for Asthma

Submitted for publication

Part V

Outlook & Overview

Effect of Transportation and Storage Using Sorbent 153 Tubes of Exhaled Breath Samples on Diagnostic

Accuracy of Electronic Nose Analysis

Journal of Breath Research (2013), 7(1): 016002

Chapter 11

Breathomics in Lung Disease 171

Chest (2015), accepted for publication

Chapter 12

The Scent of Colorectal Cancer: Detection by Volatile 189 Organic Compound Analysis

Clinical Gastroeneterology and Hepatology (2014), 12: 1085-89

Chapter 13 General Discussion 299 Not Published

Part VI

Addendum