Browsing by Title

Sort by: Order: Results:

Now showing items 231-250 of 1559
  • Liikanen, Ilkka (Helsingin yliopisto, 2015)
    Cancer remains a major cause of death and novel treatment modalities are needed. Oncolytic immunotherapy is a safe and promising approach, where cancer-selective viruses kill only cancer cells and mount an immune response against the tumor. We aimed to improve oncolytic adenoviral immunotherapy by combining it with chemotherapy and radiotherapy, and by identifying resistance mechanisms and biomarkers. We first showed that combining radiotherapy with adenoviral vector proteins E4orf3 and E4orf6, but not E1B55K, enhanced DNA damage accumulation and cancer cell killing, and inhibited prostate tumor growth in mice. This intrinsic ability of adenoviruses to radiosensitize cells could be harnessed against cancer cells by selective targeting, thus increasing efficacy while reducing the harmful side-effects of radiotherapy. In study two, we established two ovarian cancer mouse models, where tumors relapse despite the presence of functional oncolytic adenovirus, with tumor stroma maintaining the virus resistance. We identified upregulated interferon signaling in the resistant tumors by microarray, while pathway analyses suggested potential therapeutic targets, and myxovirus resistance protein A (MxA) was found a protein level indicator correlating with resistance to virus. Our results provide a putative biomarker and targets, which can help in detecting and overcoming resistance against oncolytic adenovirus. Antitumor T-cell activation appears to require autophagy and immunogenic cell death (ICD). In a translational study, we demonstrated preclinically that oncolytic adenovirus together with low-dose temozolomide and cyclophosphamide increased ICD and autophagy, resulting in tumor growth inhibition. Combination therapy was found safe in 41 treatments given to patients with refractory solid tumors in the context of an advanced therapy access program (ATAP). Increase of an ICD marker protein high-mobility group box 1 (HMGB1) and antitumor T-cell activity suggested activation of immune responses. Disease stabilization or better was observed in 67% of evaluable treatments, and as an estimated effect on survival, combination-treated patients trended for increased overall survival over non-randomized control patients. Biomarkers are urgently needed for identification of cancer patients likely to benefit from immunotherapy. Because HMGB1 protein is emerging a key player in immunomodulation, we addressed the biomarker value of HMGB1 serum level in an ATAP cohort of 202 cancer patients treated with oncolytic adenoviruses: Patients with low-baseline HMGB1 showed significantly improved overall survival and disease control rate in multivariate analyses as compared to high-baseline patients. Both patient groups showed good safety. HMGB1-low patients seemed to benefit from immunogenic virus constructs and antitumor T-cell activity. Thus, we have identified HMGB1 as a novel prognostic and predictive biomarker for oncolytic immunotherapy, which may distinguish between immunologically inert and responsive cancer patients. This thesis provides rationale for combining oncolytic adenoviruses with radiotherapy, low-dose temozolomide and cyclophosphamide. We report safety, possible signs of efficacy, and immunological effects in altogether 238 patient treatments, and introduce promising biomarkers for oncolytic immunotherapy. Our results can help in designing clinical trials and developing oncolytic adenovirus treatments.
  • Hannila-Handelberg, Tuula (Helsingin yliopisto, 2009)
    Most of the diseases affecting public health, like hypertension, are multifactorial by etiology. Hypertension is influenced by genetic, life style and environmental factors. Estimation of the influence of genes to the risk of essential hypertension varies from 30 to 50%. It is plausible that in most of the cases susceptibility to hypertension is determined by the action of more than one gene. Although the exact molecular mechanism underlying essential hypertension remains obscure, several monogenic forms of hypertension have been identified. Since common genetic variations may predict, not only to susceptibility to hypertension, but also response to antihypertensive drug therapy, pharmacogenetic approaches may provide useful markers in finding relations between candidate genes and phenotypes of hypertension. The aim of this study was to identify genetic mutations and polymorphisms contributing to human hypertension, and examine their relationships to intermediate phenotypes of hypertension, such as blood pressure (BP) responses to antihypertensive drugs or biochemical laboratory values. Two groups of patients were investigated in the present study. The first group was collected from the database of patients investigated in the Hypertension Outpatient Ward, Helsinki University Central Hospital, and consisted of 399 subjects considered to have essential hypertension. Frequncies of the mutant or variant alleles were compared with those in two reference groups, healthy blood donors (n = 301) and normotensive males (n = 175). The second group of subjects with hypertension was collected prospectively. The study subjects (n=313) underwent a protocol lasting eight months, including four one-month drug treatment periods with antihypertensive medications (thiazide diuretic, β-blocker, calcium channel antagonist, and an angiotensin II receptor antagonist). BP responses and laboratory values were related to polymorphims of several candidate genes of the renin-angiotensin system (RAS). In addition, two patients with typical features of Liddle’s syndrome were screened for mutations in kidney epithelial sodium channel (ENaC) subunits. Two novel mutations causing Liddle’s syndrome were identified. The first mutation identified located in the beta-subunit of ENaC and the second mutation found located in the gamma-subunit, constituting the first identified Liddle mutation locating in the extracellular domain. This mutation showed 2-fold increase in channel activity in vitro. Three gene variants, of which two are novel, were identified in ENaC subunits. The prevalence of the variants was three times higher in hypertensive patients (9%) than in reference groups (3%). The variant carriers had increased daily urinary potassium excretion rate in relation to their renin levels compared with controls suggesting increased ENaC activity, although in vitro they did not show increased channel activity. Of the common polymorphisms of the RAS studied, angiotensin II receptor type I (AGTR1) 1166 A/C polymorphism was associated with modest changes in RAS activity. Thus, patients homozygous for the C allele tended to have increased aldosterone and decreased renin levels. In vitro functional studies using transfected HEK293 cells provided additional evidence that the AGTR1 1166 C allele may be associated with increased expression of the AGTR1. Common polymorphisms of the alpha-adducin and the RAS genes did not significantly predict BP responses to one-month monotherapies with hydroclorothiazide, bisoprolol, amlodipin, or losartan. In conclusion, two novel mutations of ENaC subunits causing Liddle’s syndrome were identified. In addition, three common ENaC polymorphisms were shown to be associated with occurrence of essential hypertension, but their exact functional and clinical consequences remain to be explored. The AGTR1 1166 C allele may modify the endocrine phenotype of hypertensive patients, when present in homozygous form. Certain widely studied polymorphisms of the ACE, angiotensinogen, AGTR1 and alpha-adducin genes did not significantly affect responses to a thiazide, β-blocker, calcium channel antagonist, and angiotensin II receptor antagonist.
  • Korvenoja, Antti (Helsingin yliopisto, 2007)
    MEG directly measures the neuronal events and has greater temporal resolution than fMRI, which has limited temporal resolution mainly due to the larger timescale of the hemodynamic response. On the other hand fMRI has advantages in spatial resolution, while the localization results with MEG can be ambiguous due to the non-uniqueness of the electromagnetic inverse problem. Thus, these methods could provide complementary information and could be used to create both spatially and temporally accurate models of brain function. We investigated the degree of overlap, revealed by the two imaging methods, in areas involved in sensory or motor processing in healthy subjects and neurosurgical patients. Furthermore, we used the spatial information from fMRI to construct a spatiotemporal model of the MEG data in order to investigate the sensorimotor system and to create a spatiotemporal model of its function. We compared the localization results from the MEG and fMRI with invasive electrophysiological cortical mapping. We used a recently introduced method, contextual clustering, for hypothesis testing of fMRI data and assessed the the effect of neighbourhood information use on the reproducibility of fMRI results. Using MEG, we identified the ipsilateral primary sensorimotor cortex (SMI) as a novel source area contributing to the somatosensory evoked fields (SEF) to median nerve stimulation. Using combined MEG and fMRI measurements we found that two separate areas in the lateral fissure may be the generators for the SEF responses from the secondary somatosensory cortex region. The two imaging methods indicated activation in corresponding locations. By using complementary information from MEG and fMRI we established a spatiotemporal model of somatosensory cortical processing. This spatiotemporal model of cerebral activity was in good agreement with results from several studies using invasive electrophysiological measurements and with anatomical studies in monkey and man concerning the connections between somatosensory areas. In neurosurgical patients, the MEG dipole model turned out to be more reliable than fMRI in the identification of the central sulcus. This was due to prominent activation in non-primary areas in fMRI, which in some cases led to erroneous or ambiguous localization of the central sulcus.
  • Rautemaa, Riina (Helsingin yliopisto, 2001)
  • Alitalo, Antti (Helsingin yliopisto, 2004)
  • Seppänen, Mikko (Helsingin yliopisto, 2007)
    The study assessed whether plasma concentrations of complement factors C3, C4, or immunoglobulins, serum classical pathway hemolytyic activity, or polymorphisms in the class I and II HLA genes, isotypes and gene numbers of C4, or allotypes of IgG1 and IgG3 heavy chain genes were associated with severe frequently recurring or chronic mucosal infections. According to strict clinical criteria, 188 consecutive voluntary patients without a known immunodeficiency and 198 control subjects were recruited. Frequencies of low levels in IgG1, IgG2, IgG3 and IgG4 were for the first time tested from adult general population and patients with acute rhinosinusitis. Frequently recurring intraoral herpes simplex type 1 infections, a rare form of the disease, was associated with homozygosity in HLA -A*, -B*, -C*, and -DR* genes. Frequently recurrent genital HSV-2 infections were associated with low levels of IgG1 and IgG3, present in 54% of the recruited patients. This association was partly allotype-dependent. The G3mg,G1ma/ax haplotype, together with low IgG3, was more common in patients than in control subjects who lacked antibodies against herpes simplex viruses. This is the first found immunogenetic deficiency in otherwise healthy adults that predisposes to highly frequent mucosal herpes recurrences. According to previous studies, HSV effectively evades the allotype G1ma/ax of IgG1, whereas G3mg is associated with low IgG3. Certain HLA genes were more common in patients than in control subjects. Having more than one C4A or C4B gene was associated with neuralgias caused by the virus. Low levels of IgA, IgG1, IgG2, IgG3, and IgG4 were common in the general adult population, but even more frequent in patients with chronic sinusitis. Only low IgG1 was more common chronic than in acute rhinosinusitis. Clinically, nasal polyposis and bronchial asthma were associated with complicated disease forms. The best differentiating immunologic parameters were C4A deficiency and the combination of low plasma IgG4 together with low IgG1 or IgG2, performing almost equally. The lack of C4A, IgA, and IgG4, all known to possess anti-inflammatory activity, together with a concurrently impaired immunity caused by low subclass levels, may predispose to chronic disease forms. In severe chronic adult periodontitis, any C4A or C4B deficiency combined was associated with the disease. The new quantitative analysis of C4 genes and the conventional C4 allotyping method complemented each other. Lowered levels of plasma C3 or C4 or both, and serum CH50 were found in herpes and periodontitis patients. In rhinosinusitis, there was a linear trend with the highest levels found in the order: acute > chronic rhinosinusitis > general population > blood donors with no self-reported history of rhinosinusitis. Complement is involved in the defense against the tested mucosal infections. Seemingly immunocompetent patients with chronic or recurrent mucosal infections frequently have subtle weaknesses in different arms of immunity. Their susceptibility to chronic disease forms may be caused by these. Host s subtly impaired immunity often coincides with effective immune evasion from the same arms of immunity by the disease-causing pathogens. The interpretation of low subclass levels, if no additional predisposing immunologic factors are tested, is difficult and of limited value in early diagnosis and treatment.
  • Bhattacharjee, Arnab (Helsingin yliopisto, 2014)
    Complement is comprised of a cascade of proteins that recognizes and attacks the invading microbes and thus is the first line of defense for the human body against invading pathogens. It is initiated via different activation pathways that lead to C3b deposition on the target and sequentially to the formation of lytic membrane attack complexes (MAC). One of the complement activation pathways the alternative pathway (AP) can be activated on any surface, self or non-self, and is therefore tightly regulated. Complement Factor H (CFH) is the most important complement down-regulator and it mediates target discrimination between self and non-self cells. Several point mutations in CFH and/or autoantibodies (AA) against it are found to be directly associated with atypical haemolytic uremic syndrome (aHUS), a severe and often fatal disease triggered by the impaired regulation of AP on self surfaces leading to complement attack. ----- CFH is composed of 20 homologous complement control protein domains (CCP). The N-terminal domains 1 to 4 (CFH1-4) mediate inactivation of C3b on the self-surfaces and the C-terminal domains 19 and 20 (CFH19-20) are critical for the ability of CFH to discriminate between self and non-self structures. Self-surfaces are rich in anionic sialic acids (SA) and glycosaminoglycans (GAGs) that are not present on pathogenic microbes. CFH19-20 contains binding sites for both the C3d part of C3b and self-surface polyanions that enhance avidity of CFH to C3b on self surfaces and thus enhance C3b inactivation. CFH mutations that have been found in aHUS patients are mostly located in CFH19-20. ----- The previously solved X-ray crystal structure of CFH19-20 illuminated the location of aHUS related mutations. The aims of this thesis work were to study the functionality of CFH on a molecular level by studying the molecular structure of CFH C-terminus and its mutants along with structures of CFH in complex with its different interacting partners, as well as the structure of the domains of CFH-related protein-1 highly homologous to CFH19-20. The structures solved and the their relevance are described in the four articles attached to this thesis. ------ In the first article, stability of the CFH C-terminus fold by aHUS mutation(s) was studied by analyzing the binding of the CFH19-20 mutant proteins to C3d/C3b using radioligand assays and affinity chromatography. The X-ray crystal structures of CFH19-20 with two different point mutations (of residues indicated to be involved in binding C3d/C3b) were solved. It was shown that these mutations did not result in the disruption of the basic fold of CFH19-20, but maintained the same fold with a prominent difference in the surface charge distribution in the zone of the residues. The results clearly indicated that the aHUS mutations on CFH do not disrupt the basic structural fold, but induce anomaly in the charge distribution of the molecule, explaining the effects of the mutations to its C3b/heparin binding abilities suggested to be critical for the pathogenesis of the disease. In the second article, we revealed the rationale of the molecular mechanism of CFH19-20 mediated self nonself discrimination and showed why point mutations in CFH19-20 lead to aHUS. The CFH19-20 :C3d structure reported in this article revealed two independent binding interfaces between CFH19-20 and C3d, namely the CFH19 site and the CFH20 site . The results of deeper analysis of this structure also showed that the simultaneous binding of the CFH19-20 via the CFH19 site to C3b and via CFH20 site to C3d was possible. In the third article, the X-ray crystal structure of CFH19-20 was solved in complex with the outer surface protein E (OspE) from Borrelia burgdorferi in order to understand the molecular mechanism of sequestering CFH by microbes which results in complement evasion. The nucleomagnetic resonance (NMR) structure of the OspE protein from Borrelia burgdorferi reported in this paper was required for solving the structure of OspE in complex with CFH19-20. Chemical shift perturbations studies using NMR also confirmed the physiological viability of the complex structure. This complex structure was the first structure of CFH19-20 in complex with any microbial protein and thus answered the puzzle of the molecular mimicry used by microbes involving CFH C-terminus in order to evade complement. ----- In the fourth article the structure of the CFHR1 domains 4 and 5 (CFHR14-5) was solved and used to explain why AA bind to a common epitope on CFH domain 20, which is highly homologous to domain 5 of CFHR1. The CFHR14-5 structure revealed an important structural bigamy of CFH and its related proteins that can be used to understand why CFHR-1 deficiency and formation of AA against CFH (CFH- AA) lead to autoimmune aHUS (AI-aHUS). We extensively studied CFH-AA from more than a dozen of patients and their binding behavior to CFH and CFHR1. The results suggest a novel hypothesis on the pathogenesis of AI-aHUS. In conclusion, the results have revealed the molecular mechanisms beneath different functionalities of the C-terminus of CFH. It is not only the most important molecule to facilitate the target discrimination by the AP, but is also a prominent tool used by the microbes in order to evade complement attack. Furthermore, the CFH C- terminus also houses the AA binding epitope and thus also plays a role in the pathogenesis of AI-aHUS. We were also quite surprised to find out that the molecular structure of CFH C-terminus is extremely stable, and hardly undergoes any changes in its conformation in the presence of other ligands. Cumulatively, the structures of the CFH in presence of its different partners of interactions contributed greatly to the knowledge pool of the understanding of the molecular mechanisms associated with CFH in complement activation and regulation in health and disease.
  • Lehtinen, Markus (Helsingin yliopisto, 2011)
    Alternative pathway (AP) of complement can be activated on any surface, self or non-self. In atypical hemolytic uremic syndrome (aHUS) the AP regulation on self surfaces is insufficient and leads to complement attack against self-cells resulting usually in end-stage renal disease. Factor H (FH) is one of the key regulators of AP activation on the self surfaces. The domains 19 and 20 (FH19-20) are critical for the ability of FH to discriminate between C3b-opsonized self and non-self surfaces and are a hot-spot for mutations that have been described from aHUS patients. FH19-20 contains binding sites for both the C3d part of C3b and self surface polyanions that are needed for efficient C3b inactivation. To study the dysfunction of FH19-20, crystallographic structures of FH19-20 and FH19-20 in complex with C3d (FH19-20:C3d) were solved and aHUS-associated and structurally interesting point mutations were induced to FH19-20. Functional defects caused by these mutations were studied by analyzing binding of the FH19-20 mutant proteins to C3d, C3b, heparin, and mouse glomerular endothelial cells (mGEnCs). The results revealed two independent binding interfaces between FH19-20 and C3d - the FH19 site and the FH20 site. Superimposition of the FH19-20:C3d complex on the previously published C3b and FH1-4:C3b structures showed that the FH20 site on C3d is partially occluded, but the FH19 site is fully available. Furthermore, binding of FH19-20 via the FH19 site to C3b did not block binding of the functionally important FH1-4 domains and kept the FH20 site free to bind heparin or an additional C3d. Binding assays were used to show that FH20 domain can bind to heparin while FH19-20 is bound to C3b via the FH19 site, and that both the FH19 site and FH20 are necessary for recognition of non-activator surfaces. Simultaneous binding of FH19 site to C3b and FH20 to anionic self structures are the key interactions in self-surface recognition by FH and thereby enhanced avidity of FH explains how AP discriminates between self and non-self. The aHUS-associated mutations on FH19-20 were found to disrupt binding of the FH19 or FH20 site to C3d/C3b, or to disrupt binding of FH20 to heparin or mGEnC. Any of these dysfunctions leads to loss of FH avidity to C3b bearing self surfaces explaining the molecular pathogenesis of the aHUS-cases where mutations are found within FH19-20.
  • Cheng, Zhu-Zhu (Helsingin yliopisto, 2005)
  • Hakulinen, Juha (Helsingin yliopisto, 2003)
  • Junnikkala, Sami (Helsingin yliopisto, 2002)
  • Bykov, Igor (Helsingin yliopisto, 2008)
    Alcoholic liver disease (ALD) is a well recognized and growing health problem worldwide. ALD advances from fatty liver to inflammation, necrosis, fibrosis and cirrhosis. There is accumulating evidence that the innate immune system is involved in alcoholic liver injury. Within the innate and acquired immune systems, the complement system participates in inflammatory reactions and in the elimination of invading foreign, as well as endogenous apoptotic or injured cells. The present study aimed at evaluating the role of the complement system in the development of alcoholic liver injury. First, in order to study the effects of chronic ethanol intake on the complement system, the deposition of complement components in liver and the expression of liver genes associated with complement in animals with alcohol-induced liver injury were examined. It was demonstrated that chronic alcohol exposure leads to hepatic deposition of the complement components C1, C3, C8 and C9 in the livers of rats. Liver gene expression analysis showed that ethanol up-regulated the expression of transcripts for complement factors B, C1qA, C2, C3 and clusterin. In contrast, ethanol down-regulated the expression of the complement regulators factor H, C4bp and factor D and the terminal complement components C6, C8α and C9. Secondly, the role of the terminal complement pathway in the development of ALD was evaluated by using rats genetically deficient in the complement component C6 (C6-/-). It was found that chronic ethanol feeding induced more liver pathology (steatosis and inflammatory changes) in C6-/- rats than in wild type rats. The hepatic triacylglyceride content and plasma alanine aminotransferase activity increased in C6-/- rats, supporting the histopathological findings and elevation of the plasma pro-/anti-inflammatory TNF-/IL-10 ratio was also more marked in C6-/- rats. Third, the role of the alternative pathway in the development of alcoholic liver steatosis was characterized by using C3-/- mice. In C3-/- mice ethanol feeding tended to reduce steatosis and had no further effect on liver triacylglyceride, liver/body weight ratio nor on liver malondialdehyde level and serum alanine aminotransferase activity. In C3-/- mice alcohol-induced liver steatosis was reduced also after an acute alcohol challenge. In both wild type and C3-/- mice ethanol markedly reduced serum cholesterol and ApoA-I levels, phospholipid transfer protein activity and hepatic mRNA levels of fatty acid binding proteins and fatty acid -oxidation enzymes. In contrast, exclusively in C3-/- mice, ethanol treatment increased serum and liver adiponectin levels but down-regulated the expression of transcripts of lipogenic enzymes, adiponectin receptor 2 and adipose differentiation-related protein and up-regulated phospholipase D1. In conclusion, this study has demonstrated that the complement system is involved in the development of alcohol-induced liver injury. Chronic alcohol exposure causes local complement activation and induction of mRNA expression of classical and alternative pathway components in the liver. In contrast expression of the terminal pathway components and soluble regulators were decreased. A deficient terminal complement pathway predisposes to alcoholic liver damage and promotes a pro-inflammatory cytokine response. Complement component C3 contributes to the development of alcohol-induced fatty liver and its consequences by affecting regulatory and specific transcription factors of lipid homeostasis.
  • Hiltunen, Laura (Helsingin yliopisto, 2014)
    Suicides and attempted suicides in relation to weather and daylight in Finland, from 1969 to 2010 Suicide statistics show higher figures during spring and summer compared to autumn and winter. No explanation to this phenomenon has been found, but seasonal changes in weather have been suspected to be involved. The objective of this study was to find out whether correlation between suicide statistics and weather variables exists in Finland. Suicide statistics from 1969 to 2010 in Finland were compared to daily, monthly, and annual weather data, on the national level as well as in the Helsinki, Jyväskylä and Oulu regions. Suicide mortality was at its highest between May 15 and July 25. During that period the day length is at its longest. No weather correlation as to that period was found. However, temperature did correlate with suicide mortality on an annual basis, and more clearly during winter; the lower the temperature was, the lower the suicide rate was. Furthermore, global solar radiation correlated negatively with suicide mortality between September and April. These correlations were more pronounced among men, and in the Helsinki region. For attempted suicides, in the Helsinki region, a correlation with atmospheric pressure was found. For women the correlation was positive, but for men, it was negative. Any biological or social mechanisms that may contribute to these correlations remain currently unknown. However, the biological intrinsic clock which follows the light-dark cycle cannot be ruled out as a biological mechanism. Furthermore, earlier studies have shown correlations between hormonal changes and weather variables. In severe depressive disorder, which is a major risk factor for suicide, disruptions in the biological rhythms, and hormone secretions do occur, but it is not known to which extent these disruptions might be triggered due to weather conditions. Therefore, more research is needed to evaluate the clinical significance and implications of these findings, and to further improve suicide prevention.
  • Tukiainen, Eija (Helsingin yliopisto, 2008)
    Acute pancreatitis (AP) is a common disease. Mild disease resolves spontaneously in a few days. Severe forms of the disease can lead to local complications, necrosis, and abscesses in and around the pancreas. Systemic inflammation in severe AP is associated with distant organ failures. The aim of this study is to identify genetically determined prognostic factors involved in the clinical features of AP. The study employs a candidate-gene approach, and the genes are involved in trysinogen activation in the initiation phase of the disease, as well as in the systemic inflammation as the disease proceeds. The last study examines adipokines, fat-derived hormones characterized with the capacity to modify inflammation. SPINK 1 is a gene coding trypsin activation inhibitor. Mutations N34S and P55N were determined by minisequencing methods in 371 AP patients and in 459 controls. The mutation N34S was more common in AP patients (7.8%) than in controls (2.6%). This suggests that SPINK 1 gene mutation N34S is a risk factor for AP. In the fourth study, in 12 matched pairs of patients with severe and mild AP, levels of adipokines, adiponectin, and leptin were evaluated. Plasma adipokine levels did not differ between patients with mild and severe AP. The results suggest that in AP, adipokine plasma levels are not factors predisposing to organ failures. This study identified the SPINK 1 mutation N34S to be a risk factor for AP in the general population. As AP is a multifactorial disease, and extensive genetic heterogeneity is likely, further identification of genetic factors in the disease requires larger future studies with more advanced genetic study models. Further identification of the patient characteristics associated with organ failures offers another direction of the study to achieve more detailed understanding of the severe form of AP.
  • Ovaska, Mikko (Helsingin yliopisto, 2014)
    Mikko Ovaska. Complications in Ankle Fracture Surgery. Helsinki Bone and Joint Research Group, Department of Orthopaedic Surgery and Traumatology, Faculty of Medicine, University of Helsinki, Finland. Helsinki 2014. Ankle fractures are among the most frequently encountered surgically treated fractures. The operative treatment of this fracture may be associated with several complications. The most frequently encountered complications are related wound healing, and deep infection may have devastating consequences. As the population continues to age, the number of elderly patients with comorbidities sustaining ankle fractures continues to rise. In the future, an increase in complications related to ankle fracture surgery is expected. The purpose of this study was to investigate complications related to ankle fracture surgery. The study population consisted of 5123 consecutive ankle fracture patients, who were operatively treated at a level I-trauma center during the years 2002─2011. The study aimed to determine the most common technical errors resulting in early reoperation following ankle fracture surgery, and to identify the most important risk factors for deep surgical site infection (SSI) following operative treatment of ankle fractures. Additionally, the study aimed to assess the outcome of patients treated with flap reconstruction following deep infection with exposed hardware, and recognize the main factors predisposing to a treatment failure of an infected ankle fracture. The study showed that problems related to syndesmotic reduction together with fibular shortening were the most important indications for early reoperation following ankle fracture surgery. Several modifiable risk factors for deep infection were identified; most importantly, the multivariable analysis showed that smoking (OR = 3.7, 95% CI 1.6-8.5), and duration of surgery > 90 minutes (OR = 2.5, 1.1-5.7) were independent risk factors for deep infection. Cast application in the operating room was independently associated with a decreased infection rate (OR = 0.4, 95% CI 0.2-0.8). The study also revealed that soft-tissue defects around ankle with infected hardware can be successfully treated with local flaps. However, flap-related complications are common. Despite eventual reconstructive success, patients perceive a poorer health-related quality of life than the general population, and only half of them recover their pre-injury level of function. The study confirmed the hypothesis that hardware removal prior to fracture union leads to a poor clinical outcome following deep ankle fracture infection (OR = 3.3, 95% CI 1.0-10.7). The devastating nature of deep infection following operative treatment of an ankle fracture emphasizes the crucial role of preventive measures. Therefore, recognition of red flags such as diabetes, smoking, alcohol abuse, and compromised soft tissue condition is of paramount importance. Reinforcing the surgical armamentarium with meticulous preoperative planning and implementation of a check-list together with recognition of the most common surgical errors may be valuable adjuncts in reducing the number of complications. Deep infections following ankle fracture surgery are best managed by a multidisciplinary musculoskeletal infection team. Keywords: ankle fracture, reoperation, surgical site infection, complication, flap reconstruction.
  • Lahesmaa-Korpinen, Anna-Maria (Helsingin yliopisto, 2012)
    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.
  • Ovaska, Kristian (Helsingin yliopisto, 2014)
    Cancers are a heterogeneous group of diseases that cause 7.6 million deaths yearly worldwide. At the cellular level, cancer is characterized by increased proliferation and invasion of tissue. These phenotypes are caused by environmental or inherited factors that increase the mutability of the genome, leading to dysregulation of a number of cellular processes. Identifying the genotypic changes and their phenotypic consequences is key to accurate diagnosis and prognosis, as well as improved treatment regimens. Cancer cells can be investigated at a genome-wide scale using high-throughput measurement techniques such as DNA sequencing and microarrays. These rapidly evolving technologies provide experimental data that have two challenging characteristics: the volume of data is large and data are structurally complex. These data need to be analyzed in an accurate and scalable manner to arrive at biomedically relevant conclusions. I have developed three computational methods for analyzing high-throughput genomic data, and applied the methods to experimental data from three cancers. The first computational method is an extensible workflow framework, Anduril, for organizing the overall software structure of an analysis in a scalable manner. The second method, SPINLONG, is a flexible algorithm for analyzing chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) data from complex experimental designs, such as time series measurements of multiple markers. The third method, GROK, is used for preprocessing deep sequencing data. Its design is based on a mathematical formalism that provides a succinct language for these operations. The experimental part studies gene regulation and expression in glioblastoma multiforme, and breast and prostate cancer. The results demonstrate the applicability of the developed methods to cancer research and provide insights into the dysregulation of gene expression in cancer. All three studies use both cell line and clinical material to connect the molecular and disease outcome aspects of cancer. These experiments yield results at two conceptual levels. At the holistic level, lists of significant genes or genomic regions provide a genome-wide view into genomic alterations in cancer. At the specific level, we focus on one or a few central genes, which are experimentally validated, to provide an accessible starting point for understanding the results. Together, the thesis focuses on understanding the complexity of cancer and managing the complexity of genome-wide data.
  • Karinen, Sirkku (Helsingin yliopisto, 2013)
    Phenotype is a collection of an organism's observable features that can be characterized both on individual level and on single cell level. Phenotypes are largely determined by their molecular processes which also explains their inheritance and plasticity. Some of the molecular background of phenotypes can be characterized by inherited genetic variations and alterations in gene expression. The high-throughput measurement technologies enable the measurement of molecular determinants in cells. However, measurement technologies produce remarkable large data sets and the research questions have become increasingly complex. Thus computational methods are needed to discover molecular mechanisms behind the phenotypes. In many cases, analysis of molecular determinants that contribute to the phenotype proceeds by first identifying putative candidates by using a priori information and high-throughput measurements. Then further analysis can focus on most promising molecules. In many cases, the aim is to identify relevant markers or targets from a set of candidate molecules. Often biomedical studies result in a long list of candidate genes, and to interpret these candidates, information on their context in cell functions is needed. This context information can give insight to synergistic effects of molecular machinery in cells when functions of individual molecules do not explain the observed phenotype. In addition, the context information can be used to generate candidates. One of the methods in this thesis provides a computational data integration method that provides a link in between candidate genes from molecular pathways and genetic variants. It uses publicly available biological knowledge bases to systematically create functional context of candidate genes. This approach is especially important when studying cancer, that is dependent of complex molecular signaling. Genotypes associated with inherited disease predispositions have been studied successfully in the past, however, traditional methods are not applicable in wide variety of analysis conditions. Thus, this thesis introduces a method that uses haplotype sharing to identify genetic loci inherited by multiple distantly related individuals. It is flexible and can be used in various settings, also with very limited number of samples. Increasing the number of biological replicates in gene expression analysis increases the reliability of the results. In many cases, however, the number of samples is limited. Therefore, pooling gene expression data from multiple published studies can increase the understanding of the molecular background behind cell types. This is shown in this thesis by an analysis that identifies gene expression differences in two cell types using publicly available gene expression samples from previous studies. Finally, when candidate molecules are available to characterize phenotypes, they can be compiled into biomarkers. In many cases, a combination of multiple molecules serves as a better biomarker than a single molecule. This thesis also includes a machine learning approach that is used to discover a classifier that predicts the phenotype.