Abstract Advances in perinatal treatment practices—such as antenatal corticosteroids, surfactant replacement therapy, and gentler ventilator modalities—have improved the survival of infants born preterm. Consequently, later morbidity and pulmonary outcome for survivors has attracted increasing interest. The incidence of bronchopulmonary dysplasia (BPD) remains high and the condition is manifesting in infants born at earlier gestational weeks than before. This so-called new BPD results from the arrest of alveolar development and is associated with less structural airway injury and interstitial fibrosis than previously. Long-term follow-up data on lung function, lung structure and respiratory morbidity of children treated with modern methods is insufficiently known. We performed a follow-up study of 88 preterm-born children and 88 matched term-born controls at school age. Children born preterm had lower values in lung function measurements than term-born peers. Reductions were most marked in those with a history of BPD. In accordance with the foetal origins hypothesis, children with intrauterine growth restriction (IUGR) had lower lung function than gestation-controls. This indicates that poor growth in utero is an additional burden on pulmonary health. Both IUGR and BPD predicted lower lung function independently. High-resolution computed tomography of the lung was obtained from 21 children with a history of BPD. Structural abnormalities were common, children with severe BPD being most affected. Preterm children were hospitalised more often than controls, mainly because of wheezing disorders. However, BPD did not influence the hospitalisations. According to the meta-analysis of the contemporary data available, the respiratory outcome of children who had only mild BPD may have improved in comparison to old follow-up data, whereas the results for those without BPD or moderate-to-severe BPD have remained remarkably stable despite progress in treatment practices during early life. In conclusion, preterm children had subtle impairments in lung function at school age. Although they were fairly asymptomatic, concern about the possible long-term effects of preterm birth on pulmonary health is justified. It has been proposed that BPD may predispose individuals to an early COPD-like disorder. Preterm children must be protected from any additional burden on respiratory health and should be monitored appropriately for early detection of lung disease. / Tiivistelmä Keskosten tehohoito on kehittynyt viime vuosikymmeninä merkittävästi, ja yhä epäkypsempänä syntyvät keskoset selviävät hengissä syntymän jälkeen. Keskosten pitkäaikainen keuhkosairaus, bronkopulmonaalinen dysplasia (BPD), on perinteisesti johtunut hengityskonehoidon ja happikaasun aiheuttamasta keuhkovauriosta ja johtanut keuhkokudoksen arpeutumiseen. Aiempaa ennenaikaisemmilla keskosilla esiintyy kuitenkin nykyään niin sanottua uutta BPD:tä, jonka ajatellaan johtuvan enemmän keuhkorakkuloiden kehityshäiriöstä kuin hoitojen aiheuttamasta keuhkovauriosta. Selvitimme, miten nykyaikaisilla menetelmillä hoidettujen keskosten keuhkojen rakenne ja toiminta kehittyvät kouluikään mennessä. Seurantatutkimukseemme osallistui 88 ennenaikaisena syntynyttä, kouluikään ehtinyttä lasta ja 88 täysiaikaisena syntynyttä, kaltaistettua verrokkia. Keskosena syntyneiden lasten keuhkofunktio oli kouluiässä huonompi kuin täysiaikaisena syntyneiden verrokkien. Alhaisin keuhkofunktio oli niillä keskosena syntyneillä lapsilla, jotka olivat sairastaneet vastasyntyneenä BPD:n. Myös kohdunsisäiseen kasvuhäiriöön (intrauterine growth restriction, IUGR) liittyi alentunut keuhkofunktio. BPD ja IUGR ennustivat alentunutta keuhkofunktiota toisistaan riippumatta. Tutkimuksessa tehtiin myös keuhkojen ohutleiketietokonekuvaus 21 keskoselle, jotka olivat sairastaneet BPD:n. Lähes kaikilla havaittiin poikkeavia löydöksiä – eniten niillä, joilla oli ollut vastasyntyneenä BPD:n vaikea tautimuoto. Keskosina syntyneet joutuivat kahden ensimmäisen vuoden aikana verrokkeja useammin sairaalahoitoon. Yleisimpiä syitä olivat hengityksen vinkumista aiheuttavat taudit kuten ilmatiehyttulehdus, ahtauttava keuhkoputkitulehdus tai akuutti astmakohtaus. Vastasyntyneenä sairastettu BPD ei kuitenkaan lisännyt todennäköisyyttä joutua sairaalahoitoon. Tutkimuksessa tehtiin myös meta-analyysi nykyaikaisilla menetelmillä hoidettujen keskosten keuhkofunktiosta: lievää BPD:tä sairastavien tulokset näyttävät parantuneen, kun taas keskivaikeaa tai vaikeaa tautimuotoa sairastavien ja ilman BPD:tä selvinneiden keuhkofunktio ei ole muuttunut uusien hoitojen myötä. Yhteenvetona voidaan todeta, että keskosten keuhkojen toimintakyky on jonkin verran alentunut täysiaikaisiin verrattuna. Lievästi alentunut keuhkofunktio ei kuitenkaan yleensä aiheuttanut koululaisille oireita. Keskosena syntyneiden lasten hengityselinten toimintaa on syytä seurata, sillä niin sanotun uuden BPD:n pitkäaikaisesta ennusteesta ei ole vielä tietoa.

Metabolomics is the methodical scientific study of biochemical processes associated with the metabolome—which comprises the entire collection of metabolites in any biological entity. Metabolome changes occur as a result of modifications in the genome and proteome, and are, therefore, directly related to cellular phenotype. Thus, metabolomic analysis is capable of providing a snapshot of cellular physiology. Untargeted metabolomics is an impartial, all-inclusive approach for detecting as many metabolites as possible without a priori knowledge of their identity. Hence, it is a valuable exploratory tool capable of providing extensive chemical information for discovery and hypothesis-generation regarding biochemical processes. A history of metabolomics and advances in the field corresponding to improved analytical technologies are described in Chapter 1 of this dissertation. Additionally, Chapter 1 introduces the analytical workflows involved in untargeted metabolomics research to provide a foundation for Chapters 2 – 5. Part I of this dissertation which encompasses Chapters 2 – 3 describes the utilization of mass spectrometry (MS)-based untargeted metabolomic analysis to acquire new insight into cancer detection. There is a knowledge deficit regarding the biochemical processes of the origin and proliferative molecular mechanisms of many types of cancer which has also led to a shortage of sensitive and specific biomarkers. Chapter 2 describes the development of an in vitro diagnostic multivariate index assay (IVDMIA) for prostate cancer (PCa) prediction based on ultra performance liquid chromatography-mass spectrometry (UPLC-MS) metabolic profiling of blood serum samples from 64 PCa patients and 50 healthy individuals. A panel of 40 metabolic spectral features was found to be differential with 92.1% sensitivity, 94.3% specificity, and 93.0% accuracy. The performance of the IVDMIA was higher than the prevalent prostate-specific antigen blood test, thus, highlighting that a combination of multiple discriminant features yields higher predictive power for PCa detection than the univariate analysis of a single marker. Chapter 3 describes two approaches that were taken to investigate metabolic patterns for early detection of ovarian cancer (OC). First, Dicer-Pten double knockout (DKO) mice that phenocopy many of the features of metastatic high-grade serous carcinoma (HGSC) observed in women were studied. Using UPLC-MS, serum samples from 14 early-stage tumor DKO mice and 11 controls were analyzed. Iterative multivariate classification selected 18 metabolites that, when considered as a panel, yielded 100% accuracy, sensitivity, and specificity for early-stage HGSC detection. In the second approach, serum metabolic phenotypes of an early-stage OC pilot patient cohort were characterized. Serum samples were collected from 24 early-stage OC patients and 40 healthy women, and subsequently analyzed using UPLC-MS. Multivariate statistical analysis employing support vector machine learning methods and recursive feature elimination selected a panel of metabolites that differentiated between age-matched samples with 100% cross-validated accuracy, sensitivity, and specificity. This small pilot study demonstrated that metabolic phenotypes may be useful for detecting early-stage OC and, thus, supports conducting larger, more comprehensive studies. Many challenges exist in the field of untargeted metabolomics. Part II of this dissertation which encompasses Chapters 4 – 5 focuses on two specific challenges. While metabolomic data may be used to generate hypothesis concerning biological processes, determining causal relationships within metabolic networks with only metabolomic data is impractical. Proteins play major roles in these networks; therefore, pairing metabolomic information with that acquired from proteomics gives a more comprehensive snapshot of perturbations to metabolic pathways. Chapter 4 describes the integration of MS- and NMR-based metabolomics with proteomics analyses to investigate the role of chemically mediated ecological interactions between Karenia brevis and two diatom competitors, Asterionellopsis glacialis and Thalassiosira pseudonana. This integrated systems biology approach showed that K. brevis allelopathy distinctively perturbed the metabolisms of these two competitors. A. glacialis had a more robust metabolic response to K. brevis allelopathy which may be a result of its repeated exposure to K. brevis blooms in the Gulf of Mexico. However, K. brevis allelopathy disrupted energy metabolism and obstructed cellular protection mechanisms including altering cell membrane components, inhibiting osmoregulation, and increasing oxidative stress in T. pseudonana. This work represents the first instance of metabolites and proteins measured simultaneously to understand the effects of allelopathy or in fact any form of competition. Chromatography is traditionally coupled to MS for untargeted metabolomics studies. While coupling chromatography to MS greatly enhances metabolome analysis due to the orthogonality of the techniques, the lengthy analysis times pose challenges for large metabolomics studies. Consequently, there is still a need for developing higher throughput MS approaches. A rapid metabolic fingerprinting method that utilizes a new transmission mode direct analysis in real time (TM-DART) ambient sampling technique is presented in Chapter 5. The optimization of TM-DART parameters directly affecting metabolite desorption and ionization, such as sample position and ionizing gas desorption temperature, was critical in achieving high sensitivity and detecting a broad mass range of metabolites. In terms of reproducibility, TM-DART compared favorably with traditional probe mode DART analysis, with coefficients of variation as low as 16%. TM-DART MS proved to be a powerful analytical technique for rapid metabolome analysis of human blood sera and was adapted for exhaled breath condensate (EBC) analysis. To determine the feasibility of utilizing TM-DART for metabolomics investigations, TM-DART was interfaced with traveling wave ion mobility spectrometry (TWIMS) time-of-flight (TOF) MS for the analysis of EBC samples from cystic fibrosis patients and healthy controls. TM-DART-TWIMS-TOF MS was able to successfully detect cystic fibrosis in this small sample cohort, thereby, demonstrating it can be employed for probing metabolome changes. Finally, in Chapter 6, a perspective on the presented work is provided along with goals on which future studies may focus.