Computational approaches in high-throughput proteomics data analysis

Proteins are key components in biological systems as they mediate the signaling responsible for information processing in a cell and organism. In biomedical research, one goal is to elucidate the mechanisms of cellular signal transduction pathways to identify possible defects that cause disease. Advancements in technologies such as mass spectrometry and flow cytometry enable the measurement of multiple proteins from a system. Proteomics, or the large-scale study of proteins of a system, thus plays an important role in biomedical research. The analysis of all high-throughput proteomics data requires the use of advanced computational methods. Thus, the combination of bioinformatics and proteomics has become an important part in research of signal transduction pathways. The main objective in this study was to develop and apply computational methods for the preprocessing, analysis and interpretation of high-throughput proteomics data. The methods focused on data from tandem mass spectrometry and single cell flow cytometry, and integration of proteomics data with gene expression microarray data and information from various biological databases. Overall, the methods developed and applied in this study have led to new ways of management and preprocessing of proteomics data. Additionally, the available tools have successfully been used to help interpret biomedical data and to facilitate analysis of data that would have been cumbersome to do without the use of computational methods.Proteiineilla on tärkeä merkitys biologisissa systeemeissä sillä ne koordinoivat erilaisia solujen ja organismien prosesseja. Yksi biolääketieteellisen tutkimuksen tavoitteista on valottaa solujen viestintäreittejä ja niiden toiminnassa tapahtuvia muutoksia eri sairauksien yhteydessä, jotta tällaisia muutoksia voitaisiin korjata. Proteomiikka on proteiinien laajamittaista tutkimista solusta, kudoksesta tai organismista. Proteomiikan menetelmät kuten massaspektrometria ja virtaussytometria ovat keskeisiä biolääketieteellisen tutkimuksen menetelmiä, joilla voidaan mitata näytteestä samanaikaisesti useita proteiineja. Nykyajan kehittyneet proteomiikan mittausteknologiat tuottavat suuria tulosaineistoja ja edellyttävät laskennallisten menetelmien käyttöä aineiston analyysissä. Bioinformatiikan menetelmät ovatkin nousseet tärkeäksi osaksi proteomiikka-analyysiä ja viestintäreittien tutkimusta. Tämän tutkimuksen päätavoite oli kehittää ja soveltaa tehokkaita laskennallisia menetelmiä laajamittaisten proteomiikka-aineistojen esikäsittelyyn, analyysiin ja tulkintaan. Tässä tutkimuksessa kehitettiin esikäsittelymenetelmä massaspektrometria-aineistolle sekä automatisoitu analyysimenetelmä virtaussytometria-aineistolle. Proteiinitason tietoa yhdistettiin mittauksiin geenien transkriptiotasoista ja olemassaolevaan biologisista tietokannoista poimittuun tietoon. Väitöskirjatyö osoittaa, että laskennallisilla menetelmillä on keskeinen merkitys proteomiikan aineistojen hallinnassa, esikäsittelyssä ja analyysissä. Tutkimuksessa kehitetyt analyysimenetelmät edistävät huomattavasti biolääketieteellisen tiedon laajempaa hyödyntämistä ja ymmärtämistä

Integrated data management and validation platform for phosphorylated tandem mass spectrometry data

MS/MS is a widely used method for proteome-wide analysis of protein expression and PTMs. The thousands of MS/MS spectra produced from a single experiment pose a major challenge for downstream analysis. Standard programs, such as MASCOT, provide peptide assignments for many of the spectra, including identification of PTM sites, but these results are plagued by false-positive identifications. In phosphoproteomic experiments, only a single peptide assignment is typically available to support identification of each phosphorylation site, and hence minimizing false positives is critical. Thus, tedious manual validation is often required to increase confidence in the spectral assignments. We have developed phoMSVal, an open-source platform for managing MS/MS data and automatically validating identified phosphopeptides. We tested five classification algorithms with 17 extracted features to separate correct peptide assignments from incorrect ones using over 2600 manually curated spectra. The naïve Bayes algorithm was among the best classifiers with an AUC value of 97% and PPV of 97% for phosphotyrosine data. This classifier required only three features to achieve a 76% decrease in false positives as compared with MASCOT while retaining 97% of true positives. This algorithm was able to classify an independent phosphoserine/threonine data set with AUC value of 93% and PPV of 91%, demonstrating the applicability of this method for all types of phospho-MS/MS data. PhoMSVal is available at http://csbi.ltdk.helsinki.fi/phomsval.National Science Foundation (U.S.). Graduate Research Fellowship Progra

Second-generation antipsychotics and pregnancy complications

Purpose To study if second-generation antipsychotic (S-GA) use during pregnancy is associated with an increased risk of pregnancy and neonatal complications. Methods A population-based birth cohort study using national register data extracted from the "Drugs and Pregnancy" database in Finland, years 1996-2016. The sampling frame included 1,181,090 pregnant women and their singleton births. Women were categorized into three groups: exposed to S-GAs during pregnancy (n = 4225), exposed to first-generation antipsychotics (F-GAs) during pregnancy (n = 1576), and unexposed (no purchases of S-GAs or F-GAs during pregnancy, n = 21,125). Pregnancy outcomes in S-GA users were compared with those in the two comparison groups using multiple logistic regression models. Results Comparing S-GA users with unexposed ones, the risk was increased for gestational diabetes (adjusted odds ratio, OR 1.43; 95% CI 1.25-1.65), cesarean section (OR 1.35; 95% CI 1.18-1.53), being born large for gestational age (LGA) (OR 1.57; 95% CI 1.14-2.16), and preterm birth (OR 1.29; 95% CI 1.03-1.62). The risk for these outcomes increased further with continuous S-GA use. Infants in the S-GA group were also more likely to suffer from neonatal complications. Comparing S-GA users with the F-GA group, the risk of cesarean section and LGA was higher (OR 1.25, 95% CI 1.03-1.51; and OR 1.89, 95% CI 1.20-2.99, respectively). Neonatal complications did not differ between the S-GA and F-GA groups. Conclusions Prenatal exposure to S-GAs is associated with an increased risk of pregnancy complications related to impaired glucose metabolism. Neonatal problems are common and occur similarly in S-GA and F-GA users.Peer reviewe

Raskaudenaikainen lääkkeidenkäyttö, syntyneiden lasten perinataaliterveys sekä epämuodostumat 1996-2010

Raskaudenaikaisen lääkkeidenkäytön vaikutuksista sikiöön tiedetään vähän. Vain muutamien lääkkeiden tiedetään varmasti aiheuttavan sikiövaurioita, mutta toisaalta vain harvan lääkkeen tiedetään olevan turvallinen raskauden aikana käytettynä. Käyttöön tulee jatkuvasti uusia lääkkeitä, joiden kohdalla tieto raskaudenaikaisen käytön turvallisuudesta perustuu vain eläinkokeisiin. Eläinkokeet ovat suuntaa-antavia, mutta niiden tuloksia ei voida suoraan soveltaa ihmiseen. Eettiset syyt rajoittavat mahdollisuuksia tutkia lääkkeiden käyttöä raskaana olevilla naisilla ennen lääkkeen myyntiluvan myöntämistä. Tässä raportissa kuvataan raskaudenaikaista lääkkeidenkäyttöä ja sen vaikutuksia vastasyntyneiden terveyteen ja epämuodostumien esiintyvyyteen syntyneillä lapsilla tai keskeytetyissä raskauksissa vuosina 1996 2010 Suomessa. Tämä Lääkealan turvallisuus- ja kehittämiskeskus Fimean, Kelan ja Terveyden ja hyvinvoinnin laitoksen (THL) yhteistyötutkimus perustuu kansallisiin terveysrekistereihin: THL:n ylläpitämien syntymä-, raskaudenkeskeyttämis- ja epämuodostumarekisterien sekä Kelan reseptitiedoston ja erityiskorvausoikeuksien tiedoston tietoihin

Placental transporter-mediated drug interactions and offspring congenital anomalies

AimsP‐glycoprotein (P‐gp) and breast cancer resistance protein (BCRP) are efflux transporters expressed in the placenta, limiting their substrates from reaching the foetus. Our aim was to investigate if concomitant prenatal exposure to several substrates or inhibitors of these transporters increases the risk of congenital anomalies.MethodsThe national Drugs and Pregnancy database, years 1996–2014, was utilized in this population‐based birth cohort study. In the database, the Medical Birth Register, the Register on Induced Abortions, the Malformation register and the Register on Reimbursed Drug Purchases have been linked. The University of Washington Metabolism and Transport Drug Interaction Database was used to identify substrates and inhibitors of P‐gp and BCRP. We included singleton pregnancies ending in birth or elective termination of pregnancy due to foetal anomaly. Known teratogens were excluded. We identified women exposed 1 month before pregnancy or during the first trimester to P‐gp/BCRP polytherapy (n = 21 186); P‐gp/breast cancer resistance protein monotherapy (n = 97 906); non‐P‐gp/BCRP polytherapy (n = 78 636); and unexposed (n = 728 870). We investigated the association between the exposure groups and major congenital anomalies using logistic regression adjusting for several confounders.ResultsThe prevalence of congenital anomalies was higher in the P‐gp/BCRP polytherapy group (5.5%) compared to the P‐gp/BCRP monotherapy (4.7%, OR 1.13; 95% CI 1.05–1.21), the non‐P‐gp/BCRP polytherapy (4.9%, OR 1.14; 95% CI 1.06–1.22), and to the unexposed groups (4.2%, OR 1.23; 95% CI 1.15–1.31).ConclusionThe results suggest a role of placental transporter‐mediated drug interactions in teratogenesis.</p

Maternal asthma is associated with increased risk of perinatal mortality

Background Asthma is the most common chronic disease during pregnancy and it may have influence on pregnancy outcome. Objectives Our goal was to assess the association between maternal asthma and the perinatal risks as well as possible effects of asthma medication. Methods The study was based on a nationwide Finnish register-based cohort between the years 1996 and 2012 in the Drug and Pregnancy Database. The register data comprised 962 405 singleton live and stillbirths, 898 333 (93.3%) pregnancies in mothers with neither confirmed asthma nor use of asthma medication (controls), and 26 674 (2.8%) pregnancies with confirmed maternal asthma. 71% of mothers with asthma used asthma medication. The diagnosis of asthma was based on the mothers' right for subsidised medication which is carefully evaluated by strict criteria including pulmonary function testing. Odds ratio was used in comparison. Premature birth (PB), low birth weight, small for gestational age (SGA), neonatal death were the main outcome measures. Results Maternal asthma was associated with adjusted odds ratios (aORs) for perinatal mortality 1.24 (95% CI 1.05 to 1.46), preterm birth 1.18 (1.11 to 1.25), low birth weight 1.29 (1.21 to 1.37), fetal growth restriction (SGA) 1.32, (1.24 to 1.40), and asphyxia 1.09 (1.02 to 1.17). Asthma treatment reduced the increased risk of preterm birth aOR 0.85 (95% CI 0.76 to 0.96) but mothers with treated asthma had higher risks of fetal growth restriction (SGA) aOR 1.26 (1.10 to 1.45), and asphyxia aOR 1.37 (1.17 to 1.61) than mothers with untreated asthma. Conclusion Asthma is associated with increased risks of perinatal mortality, preterm birth, low birth weight, fetal growth restriction (SGA), and asphyxia. Asthma treatment reduces the risk of preterm delivery, but it does not seem to reduce other complications such as perinatal mortality.Peer reviewe

Prevalence and risk factors of radial ray deficiencies: A population-based case-control study

Radial ray deficiency is the most common congenital deficiency of the upper limb. The aim of our study was to investigate maternal risk factors for radial ray deficiencies. We conducted a nationwide population-based case-control study using national registers. All cases with a radial ray deficiency born between 1996 and 2008 were included in the study and compared with five controls without limb deficiency. In total, 115 (10 isolated, 18 with multiple congenital anomalies, and 87 syndromic) cases with radial ray deficiencies were identified and compared with 575 matched controls. The total prevalence in Finland was 1.22 per 10,000 births. No significant risk factors were observed for nonsyndromic cases. In the syndromic group, advanced maternal age (>= 35 years) increased the risk of radial aplasia (aOR 2.45, 95% CI 1.37-4.36), and a similar association was observed with multiple pregnancy (aOR 2.97, 1.16-7.62) and male sex (aOR 1.96, 1.18-3.25). Valproic acid was also a risk factor (p = .002). In conclusion, novel associations in the syndromic group of advanced maternal age and multiple pregnancy and increased risk of radial ray deficiencies were observed. Also, early reports on increased risk of RRD associated with valproate and male sex were supported by our results.</p

Second-generation antipsychotics and pregnancy complications

Purpose To study if second-generation antipsychotic (S-GA) use during pregnancy is associated with an increased risk of pregnancy and neonatal complications. Methods A population-based birth cohort study using national register data extracted from the "Drugs and Pregnancy" database in Finland, years 1996-2016. The sampling frame included 1,181,090 pregnant women and their singleton births. Women were categorized into three groups: exposed to S-GAs during pregnancy (n = 4225), exposed to first-generation antipsychotics (F-GAs) during pregnancy (n = 1576), and unexposed (no purchases of S-GAs or F-GAs during pregnancy, n = 21,125). Pregnancy outcomes in S-GA users were compared with those in the two comparison groups using multiple logistic regression models. Results Comparing S-GA users with unexposed ones, the risk was increased for gestational diabetes (adjusted odds ratio, OR 1.43; 95% CI 1.25-1.65), cesarean section (OR 1.35; 95% CI 1.18-1.53), being born large for gestational age (LGA) (OR 1.57; 95% CI 1.14-2.16), and preterm birth (OR 1.29; 95% CI 1.03-1.62). The risk for these outcomes increased further with continuous S-GA use. Infants in the S-GA group were also more likely to suffer from neonatal complications. Comparing S-GA users with the F-GA group, the risk of cesarean section and LGA was higher (OR 1.25, 95% CI 1.03-1.51; and OR 1.89, 95% CI 1.20-2.99, respectively). Neonatal complications did not differ between the S-GA and F-GA groups. Conclusions Prenatal exposure to S-GAs is associated with an increased risk of pregnancy complications related to impaired glucose metabolism. Neonatal problems are common and occur similarly in S-GA and F-GA users.</p

Risk Factors and Prevalence of Limb Deficiencies Associated With Amniotic Band Sequence: A Population-based Case-control Study

Background: Limb deficiencies associated with amniotic bands comprise a wide range of congenital anomalies. The association of maternal medication and the risk of amniotic band sequence (ABS) has not yet been addressed. Methods: This nationwide population-based case-control study used national registers on congenital anomalies, births and induced abortions, cross-linked with information on maternal prescription medicine use obtained from the registers on Reimbursed Drug Purchases and Medical Special Reimbursements. All cases with congenital limb deficiency associated with amniotic bands born between 1996 and 2008 were included in the study. Five controls without limb deficiency matched for residency and time of conception were randomly selected from the Medical Birth Register. Results: In total, 106 children with limb deficiency associated with ABS were identified and compared with 530 matched controls. Young maternal age (less than 25 y) increased the risk of limb deficiencies [odds ratio=1.72; 95% confidence interval (CI): 1.06, 2.80]. Primiparity was also associated with increased risk [adjusted odds ratio (aOR)=2.42; 95% CI: 1.52, 3.88]. After adjusting for maternal age, pregestational diabetes, and parity, maternal use of beta-blockers (adjusted OR=24.2; 95% CI: 2.57, 228) and progestogens (adjusted OR=3.79; 95% CI: 1.38, 10.4) during the first trimester of pregnancy significantly increased the risk of limb deficiencies associated with amniotic bands. Conclusions: Primiparity significantly increased the risk of limb defects associated with amniotic bands. Also, a novel association on increased risk of ABS with maternal use of progestogens or beta-blockers during the first trimester of pregnancy was observed.</p