Browsing by Subject "biomarker"

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  • Salminen, Liina; Braicu, Elena Ioana; Laaperi, Mitja; Jylha, Antti; Oksa, Sinikka; Hietanen, Sakari; Sehouli, Jalid; Kulbe, Hagen; du Bois, Andreas; Mahner, Sven; Harter, Philipp; Carpen, Olli; Huhtinen, Kaisa; Hynninen, Johanna; Hilvo, Mika (2021)
    Simple Summary Most ovarian cancer patients initially show a response to primary treatments, but the development of refractory disease is a major problem. Currently, there are no blood-based prognostic biomarkers, and the prognosis of a patient is determined by the International Federation of Gynecology and Obstetrics (FIGO) stage and residual disease after cytoreductive surgery. In this study, we developed and validated a novel test based on the ratio of two circulatory lipids that enables the prognostic stratification of ovarian cancer patients at the time of diagnosis, prior to any oncological treatments. The translational relevance of this test is to find those patients with poor prognosis early on, and to identify patients that are at high risk of recurrence despite complete cytoreduction. Thus, the test enables the early direction of novel targeted therapies to those ovarian cancer patients at greatest risk of recurrence and death. Epithelial ovarian cancer (EOC) generally responds well to oncological treatments, but the eventual development of a refractory disease is a major clinical problem. Presently, there are no prognostic blood-based biomarkers for the stratification of EOC patients at the time of diagnosis. We set out to assess and validate the prognostic utility of a novel two-lipid signature, as the lipidome is known to be markedly aberrant in EOC patients. The study consisted of 499 women with histologically confirmed EOC that were prospectively recruited at the university hospitals in Turku (Finland) and Charite (Berlin, Germany). Lipidomic screening by tandem liquid chromatography-mass spectrometry (LC-MS/MS) was performed for all baseline serum samples of these patients, and additionally for 20 patients of the Turku cohort at various timepoints. A two-lipid signature, based on the ratio of the ceramide Cer(d18:1/18:0) and phosphatidylcholine PC(O-38:4), showed consistent prognostic performance in all investigated study cohorts. In the Turku cohort, the unadjusted hazard ratios (HRs) per standard deviation (SD) (95% confidence interval) were 1.79 (1.40, 2.29) for overall and 1.40 (1.14, 1.71) for progression-free survival. In a Charite cohort incorporating only stage III completely resected patients, the corresponding HRs were 1.59 (1.08, 2.35) and 1.53 (1.02, 2.30). In linear-mixed models predicting progression of the disease, the two-lipid signature showed higher performance (beta per SD increase 1.99 (1.38, 2.97)) than cancer antigen 125 (CA-125, 1.78 (1.13, 2.87)). The two-lipid signature was able to identify EOC patients with an especially poor prognosis at the time of diagnosis, and also showed promise for the detection of disease relapse.
  • Penack, Olaf; Peczynski, Christophe; van der Werf, Steffie; Finke, Juergen; Ganser, Arnold; Schoemans, Helene; Pavlu, Jiri; Niittyvuopio, Riitta; Schroyens, Wilfried; Kaynar, Leylagul; Blau, Igor W.; van der Velden, Walter J. F. M.; Sierra, Jorge; Cortelezzi, Agostino; Wulf, Gerald; Turlure, Pascal; Rovira, Montserrat; Ozkurt, Zubeydenur; Pascual-Cascon, Maria J.; Moreira, Maria C.; Clausen, Johannes; Greinix, Hildegard; Duarte, Rafael F.; Basak, Grzegorz W. (2020)
    Elevated serum ferritin levels occur due to iron overload or during inflammation and macrophage activation. A correlation of high serum ferritin levels with increased mortality after alloSCT has been suggested by several retrospective analyses as well as by two smaller prospective studies. This prospective multicentric study aimed to study the association of ferritin serum levels before start of conditioning with alloSCT outcome. Patients with acute leukemia, lymphoma or MDS receiving a matched sibling alloSCT for the first time were considered for inclusion, regardless of conditioning. A comparison of outcomes between patients with high and low ferritin level was performed using univariate analysis and multivariate analysis using cause-specific Cox model. Twenty centers reported data on 298 alloSCT recipients. The ferritin cut off point was determined at 1500 mu g/l (median of measured ferritin levels). In alloSCT recipients with ferritin levels above cut off measured before the start of conditioning, overall survival (HR = 2.5, CI = 1.5-4.1, p = 0.0005) and progression-free survival (HR = 2.4, CI = 1.6-3.8, p <0.0001) were inferior. Excess mortality in the high ferritin group was due to both higher relapse incidence (HR = 2.2, CI = 1.2-3.8, p = 0.007) and increased non-relapse mortality (NRM) (HR = 3.1, CI = 1.5-6.4, p = 0.002). NRM was driven by significantly higher infection-related mortality in the high ferritin group (HR = 3.9, CI = 1.6-9.7, p = 0.003). Acute and chronic GVHD incidence or severity were not associated to serum ferritin levels. We conclude that ferritin levels can serve as routine laboratory biomarker for mortality risk assessment before alloSCT.
  • Bradbury, Kathryn E.; Appleby, Paul N.; Tipper, Sarah J.; Travis, Ruth C.; Allen, Naomi E.; Kvaskoff, Marina; Overvad, Kim; Tjonneland, Anne; Halkjaer, Jytte; Cervenka, Iris; Mahamat-Saleh, Yahya; Bonnet, Fabrice; Kaaks, Rudolf; Fortner, Renee T.; Boeing, Heiner; Trichopoulou, Antonia; La Vecchia, Carlo; Stratigos, Alexander J.; Palli, Domenico; Grioni, Sara; Matullo, Giuseppe; Panico, Salvatore; Tumino, Rosario; Peeters, Petra H.; Bueno-de-Mesquita, H. Bas; Ghiasvand, Reza; Veierod, Marit B.; Weiderpass, Elisabete; Bonet, Catalina; Molina, Elena; Huerta, Jose M.; Larranaga, Nerea; Barricarte, Aurelio; Merino, Susana; Isaksson, Karolin; Stocks, Tanja; Ljuslinder, Ingrid; Hemmingsson, Oskar; Wareham, Nick; Khaw, Kay-Tee; Gunter, Marc J.; Rinaldi, Sabina; Tsilidis, Konstantinos K.; Aune, Dagfinn; Riboli, Elio; Key, Timothy J. (2019)
    Insulin-like growth factor-I (IGF-I) regulates cell proliferation and apoptosis, and is thought to play a role in tumour development. Previous prospective studies have shown that higher circulating concentrations of IGF-I are associated with a higher risk of cancers at specific sites, including breast and prostate. No prospective study has examined the association between circulating IGF-I concentrations and melanoma risk. A nested case-control study of 1,221 melanoma cases and 1,221 controls was performed in the European Prospective Investigation into Cancer and Nutrition cohort, a prospective cohort of 520,000 participants recruited from 10 European countries. Conditional logistic regression was used to estimate odds ratios (ORs) for incident melanoma in relation to circulating IGF-I concentrations, measured by immunoassay. Analyses were conditioned on the matching factors and further adjusted for age at blood collection, education, height, BMI, smoking status, alcohol intake, marital status, physical activity and in women only, use of menopausal hormone therapy. There was no significant association between circulating IGF-I concentration and melanoma risk (OR for highest vs lowest fifth = 0.93 [95% confidence interval [CI]: 0.71 to 1.22]). There was no significant heterogeneity in the association between IGF-I concentrations and melanoma risk when subdivided by gender, age at blood collection, BMI, height, age at diagnosis, time between blood collection and diagnosis, or by anatomical site or histological subtype of the tumour (Pheterogeneity >= 0.078). We found no evidence for an association between circulating concentrations of IGF-I measured in adulthood and the risk of melanoma.
  • Erkan, Erdogan Pekcan; Ströbel, Thomas; Dorfer, Christian; Sonntagbauer, Markus; Weinhäusel, Andreas; Saydam, Nurten; Saydam, Okay (2019)
    Meningiomas are primary central nervous system (CNS) tumors that originate from the arachnoid cells of the meninges. Recurrence occurs in higher grade meningiomas and a small subset of Grade I meningiomas with benign histology. Currently, there are no established circulating tumor markers which can be used for diagnostic and prognostic purposes in a non-invasive way for meningiomas. Here, we aimed to identify potential biomarkers of meningioma in patient sera. For this purpose, we collected preoperative (n = 30) serum samples from the meningioma patients classified as Grade I (n = 23), Grade II (n = 4), or Grade III (n = 3). We used a high-throughput, multiplex immunoassay cancer panel comprising of 92 cancer-related protein biomarkers to explore the serum protein profiles of meningioma patients. We detected 14 differentially expressed proteins in the sera of the Grade I meningioma patients in comparison to the age- and gender-matched control subjects (n = 12). Compared to the control group, Grade I meningioma patients showed increased serum levels of amphiregulin (AREG), CCL24, CD69, prolactin, EGF, HB-EGF, caspase-3, and decreased levels of VEGFD, TGF-α, E-Selectin, BAFF, IL-12, CCL9, and GH. For validation studies, we utilized an independent set of meningioma tumor tissue samples (Grade I, n = 20; Grade II, n = 10; Grade III, n = 6), and found that the expressions of amphiregulin and Caspase3 are significantly increased in all grades of meningiomas either at the transcriptional or protein level, respectively. In contrast, the gene expression of VEGF-D was significantly lower in Grade I meningioma tissue samples. Taken together, our study identifies a meningioma-specific protein signature in blood circulation of meningioma patients and highlights the importance of equilibrium between tumor-promoting factors and anti-tumor immunity.
  • Clayton, Aled; Boilard, Eric; Buzas, Edit I; Cheng, Lesley; Falcón-Perez, Juan Manual; Gardiner, Chris; Gustafson, Dakota; Gualerzi, Alice; Hendrix, An; Hoffman, Andrew; Jones, Jennifer; Lässer, Cecilia; Lawson, Charlotte; Lenassi, Metka; Nazarenko, Irina; O’Driscoll, Lorraine; Pink, Ryan; Siljander, Pia R-M; Soekmadji, Carolina; Wauben, Marca; Welsh, Joshua A; Witwer, Ken; Zheng, Lei; Nieuwland, Rienk (2019)
    There is an increasing interest in exploring clinically relevant information that is present in body fluids, and extracellular vesicles (EVs) are intrinsic components of body fluids (?liquid biopsies?). In this report, we will focus on blood. Blood contains not only EVs but also cells, and non-EV particles including lipoproteins. Due to the high concentration of soluble proteins and lipoproteins, blood, plasma and serum have a high viscosity and density, which hampers the concentration, isolation and detection of EVs. Because most if not all studies on EVs are single-centre studies, their clinical relevance remains limited. Therefore, there is an urgent need to improve standardization and reproducibility of EV research. As a first step, the International Society on Extracellular Vesicles organized a biomarker workshop in Birmingham (UK) in November 2017, and during that workshop several working groups were created to focus on a particular body fluid. This report is the first output of the blood EV work group and is based on responses by work group members to a questionnaire in order to discover the contours of a roadmap. From the answers it is clear that most respondents are in favour of evidence-based research, education, quality control procedures, and physical models to improve our understanding and comparison of concentration, isolation and detection methods. Since blood is such a complex body fluid, we assume that the outcome of the survey may also be valuable for exploring body fluids other than blood.
  • Turck, Dominique; EFSA NDA Panel members (2017)
  • Abu-Farha, Mohamed; Tuomilehto, Jaakko; Abubaker, Jehad (2021)
  • Mahlamäki, Kasper (Helsingin yliopisto, 2019)
    Syöpätautien yleisyys lisääntyy kaikkialla maailmassa väestön vanhetessa ja Suomessakin todetaan vuosittain noin 35 000 uutta syöpää, joihin kuolee noin 13 000 henkeä. Syövän lääkehoidon painopiste on siirtymässä laajalti elimistön soluja tuhoavista sädehoidosta ja solunsalpaajista kohti potilaan omaa immuunipuolustusta syöpää vastaan ohjaavia immuno-onkologisia lääkkeitä. Immuno-onkologisilla lääkkeillä, kuten tarkastuspiste-estäjiin kuuluvilla PD-1-vasta-aineilla on saavutettu jopa pysyviä remissioita useassa vaikeahoitoisessa syövässä. Valitettavasti vain pieni osa immunologisilla syöpälääkkeillä hoidetuista potilaista saa niiden täyden hyödyn ja hoitovasteen laajentaminen koko potilasjoukkoon on osoittautunut ongelmalliseksi. Tutkielmani kirjallisuuskatsauksessa käsitellään rintasyöpää yleisesti, sekä syvennytään rintasyövän prekliinisiin tutkimusmalleihin ja rintasyöpäpotilaan immuno-onkologiavasteen ennustetekijöihin. Kokeellisen laboratoriotutkimusosuuden tavoitteina oli korreloida rintasyöpänäytteiden leukosyytti-infiltraation taso kasvaimen Myc- ja PD-L1-ekspressioon, mitata solulinjojen ja tutkimusryhmämme kehittämien PDEC-eksplanttien immuuniaktivaatiota, sekä arvioida näiden tutkimusten tulosten avulla rintasyöpäpotilaan kasvainnäytteestä kasvattamiemme PDEC-kudosviljelmien potentiaalia rintasyövän immuno-onkologisessa tutkimuksessa. Löysin tutkimalla primäärikasvainten ja PDEC-eksplanttien ominaisuuksia immunohistokemialla sekä qRT-PCR:llä korrelaation primäärikasvaimen leukosyyttimäärän sekä PDEC-viljelmien qRT-PCR:llä mitatun immuuniaktiivisuuden välille: kasvaimen korkea leukosyyttipitoisuus vaikuttaa olevan yhteydessä PDEC-viljelmien suurempaan immuuniaktiivisuuteen. Mielenkiintoista oli havaita, että vaikka immuunisolujen aktivoimiseen käytetyn Immunocultin tulisi aktivoida kaikkia T-soluja, niin edes runsas kasvaimen strooman leukosyytti-infiltraatio ei aiheuttanut qRT-PCR:llä tehdyissä immuuniaktivaatiomittauksissa menetelmän käyttöä häiritseviä vääriä positiivisia tuloksia. Tulosteni perusteella PDEC-eksplantit kykenevät kuvaamaan rintasyöpäpotilaiden kasvainkohtaisia immuuniaktivaatioeroja, mikä korostaa niiden soveltuvuutta immuno-onkologiseen tutkimukseen.
  • Puntila-Dodd, R.; Bekkevold, D.; Behrens, J. W. (Springer, 2021)
    Hydrobiologia 848: 2
    Species invasions often occur on coasts and estuaries where abiotic conditions vary, e.g. salinity, temperature, runoff etc. Successful establishment and dispersal of non-indigenous species in many such systems are poorly understood, partially since the species tend to show genetic and ecological plasticity at population level towards many abiotic conditions, including salinity tolerance. Plasticity may be driven by shifting expression of heat shock proteins such as Hsp70, which is widely recognized as indicator of physical stress. In this study, we developed a qPCR assay for expression of the hsp70 gene in the invasive round goby (Neogobius melanostomus) and tested the expression response of fish collected from a brackish environment in the western Baltic Sea to three different salinities, 0, 10 and 30. hsp70 expression was highest in fresh water, indicating higher stress, and lower at brackish (ambient condition for the sampled population) and oceanic salinities, suggestive of low stress response to salinities above the population’s current distribution. The highest stress in fresh water was surprising since populations in fresh water exist, e.g. large European rivers and Laurentian Great Lakes. The results have implications to predictions for the species’ plasticity potential and possible range expansion of the species into other salinity regimes.
  • Outinen, Tuula K.; Mantula, Paula; Jaatinen, Pia; Hämäläinen, Mari; Moilanen, Eeva; Vaheri, Antti; Huhtala, Heini; Mäkelä, Satu; Mustonen, Jukka (2019)
    Most cases of hemorrhagic fever with renal syndrome (HFRS) in Europe are caused by the Puumala hantavirus (PUUV). Typical features of the disease are increased vascular permeability, acute kidney injury (AKI), and thrombocytopenia. YKL-40 is an inflammatory glycoprotein involved in various forms of acute and chronic inflammation. In the present study, we examined plasma YKL-40 levels and the associations of YKL-40 with disease severity in acute PUUV infection. A total of 79 patients treated in Tampere University Hospital during 2005-2014 were studied. Plasma YKL-40 was measured in the acute phase, the recovery phase, and one year after hospitalization. Plasma YKL-40 levels were higher during the acute phase compared to the recovery phase and one year after hospitalization (median YKL-40 142 ng/mL, range 11-3320, vs. 45 ng/mL, range 15-529, vs. 32 ng/mL, range 3-213, p <0.001). YKL-40 level was correlated with the length of hospital stay (r = 0.229, p = 0.042), the levels of inflammatory markers-that is, blood leukocytes (r = 0.234, p = 0.040), plasma C-reactive protein (r = 0.332, p = 0.003), and interleukin-6 (r = 0.544, p <0.001), and maximum plasma creatinine level (r = 0.370, p = 0.001). In conclusion, plasma YKL-40 levels were found to be elevated during acute PUUV infection and correlated with the overall severity of the disease, as well as with the degree of inflammation and the severity of AKI.
  • Sopyllo, Konrad; Erickson, Andrew M.; Mirtti, Tuomas (2021)
    Simple Summary Prostate cancer treatment decisions are based on clinical stage and histological diagnosis, including Gleason grading assessed by a pathologist, in biopsies. Prior to staging and grading, serum or blood prostate-specific antigen (PSA) levels are measured and often trigger diagnostic examinations. However, PSA is best suited as a marker of cancer relapse after initial treatment. In this review, we first narratively describe the evolution of histological grading, the current status of Gleason pattern-based diagnostics and glance into future methodology of risk assessment by histological examination. In the second part, we systematically review the biomarkers that have been shown, independent from clinical characteristics, to correlate with clinically relevant end-points, i.e., occurrence of metastases, disease-specific mortality and overall survival after initial treatment of localized prostate cancer. Gleason grading remains the strongest prognostic parameter in localized prostate adenocarcinoma. We have here outlined the evolution and contemporary practices in pathological evaluation of prostate tissue samples for Gleason score and Grade group. The state of more observer-independent grading methods with the aid of artificial intelligence is also reviewed. Additionally, we conducted a systematic review of biomarkers that hold promise in adding independent prognostic or predictive value on top of clinical parameters, Grade group and PSA. We especially focused on hard end points during the follow-up, i.e., occurrence of metastasis, disease-specific mortality and overall mortality. In peripheral blood, biopsy-detected prostate cancer or in surgical specimens, we can conclude that there are more than sixty biomarkers that have been shown to have independent prognostic significance when adjusted to conventional risk assessment or grouping. Our search brought up some known putative markers and panels, as expected. Also, the synthesis in the systematic review indicated markers that ought to be further studied as part of prospective trials and in well characterized patient cohorts in order to increase the resolution of the current clinico-pathological prognostic factors.
  • Kiiski, Ville; Karlsson, Oskar; Remitz, Anita; Reitamo, Sakari (2015)
    Most patients with severe atopic dermatitis have elevated serum IgE levels, but there has been little research into IgE as a predictive biomarker in long-term disease outcome. The aim of this study was to evaluate the predictive value of IgE and other factors in patients with atopic dermatitis in a university clinic setting. There were 169 eligible patients (14-78 years) with a mean follow-up of 4.15 years. High baseline IgE (>= 10,000 IU/ml) was the most important patient-related factor for a poor longterm outcome, being negatively associated with good treatment response (odds ratio (OR) 0.062, p=0.002). Only 14.3% of patients with this high baseline IgE achieved a good treatment response in follow-up, compared with 79.7% in patients with lower (
  • Braicu, Elena Ioana; Darb-Esfahani, Silvia; Schmitt, Wolfgang D.; Koistinen, Kaisa M.; Heiskanen, Laura; Pöhö, Päivi; Budczies, Jan; Kuhberg, Marc; Dietel, Manfred; Frezza, Christian; Denkert, Carsten; Sehouli, Jalid; Hilvo, Mika (2017)
    Ovarian cancer is a very severe type of disease with poor prognosis. Treatment of ovarian cancer is challenging because of the lack of tests for early detection and effective therapeutic targets. Thus, new biomarkers are needed for both diagnostics and better understanding of the cellular processes of the disease. Small molecules, consisting of metabolites or lipids, have shown emerging potential for ovarian cancer diagnostics. Here we performed comprehensive lipidomic profiling of serum and tumor tissue samples from high-grade serous ovarian cancer patients to find lipids that were altered due to cancer and also associated with progression of the disease. Ovarian cancer patients exhibited an overall reduction of most lipid classes in their serum as compared to a control group. Despite the overall reduction, there were also specific lipids showing elevation, and especially alterations in ceramide and triacylglycerol lipid species were dependent on their fatty acyl side chain composition. Several lipids showed progressive alterations in patients with more advanced disease and poorer overall survival, and outperformed CA-125 as prognostic markers. The abundance of many serum lipids correlated with their abundance in tumor tissue samples. Furthermore, we found a negative correlation of serum lipids with 3-hydroxybutyric acid, suggesting an association between decreased lipid levels and fatty acid oxidation. In conclusion, here we present a comprehensive analysis of lipid metabolism alterations in ovarian cancer patients, with clinical implications.
  • Koolen, Ninah; Dereymaeker, Anneleen; Rasanen, Okko; Jansen, Katrien; Vervisch, Jan; Matic, Vladimir; De Vos, Maarten; Van Huffel, Sabine; Naulaers, Gunnar; Vanhatalo, Sampsa (2014)
  • Fortino, Vittorio; Wisgrill, Lukas; Werner, Paulina; Suomela, Sari; Linder, Nina; Jalonen, Erja; Suomalainen, Alina; Marwah, Veer; Kero, Mia; Pesonen, Maria; Lundin, Johan; Lauerma, Antti; Aalto-Korte, Kristiina; Greco, Dario; Alenius, Harri; Fyhrquist, Nanna (2020)
    Contact dermatitis tremendously impacts the quality of life of suffering patients. Currently, diagnostic regimes rely on allergy testing, exposure specification, and follow-up visits; however, distinguishing the clinical phenotype of irritant and allergic contact dermatitis remains challenging. Employing integrative transcriptomic analysis and machine-learning approaches, we aimed to decipher disease-related signature genes to find suitable sets of biomarkers. A total of 89 positive patch-test reaction biopsies against four contact allergens and two irritants were analyzed via microarray. Coexpression network analysis and Random Forest classification were used to discover potential biomarkers and selected biomarker models were validated in an independent patient group. Differential gene-expression analysis identified major gene-expression changes depending on the stimulus. Random Forest classification identified CD47, BATF, FASLG, RGS16, SYNPO, SELE, PTPN7, WARS, PRC1, EXO1, RRM2, PBK, RAD54L, KIFC1, SPC25, PKMYT, HISTH1A, TPX2, DLGAP5, TPX2, CH25H, and IL37 as potential biomarkers to distinguish allergic and irritant contact dermatitis in human skin. Validation experiments and prediction performances on external testing datasets demonstrated potential applicability of the identified biomarker models in the clinic. Capitalizing on this knowledge, novel diagnostic tools can be developed to guide clinical diagnosis of contact allergies.
  • Xu, Xiaomeng; Barreiro, Karina; Musante, Luca; Kretz, Oliver; Lin, Hanfei; Zou, Hequn; Huber, Tobias B.; Holthofer, Harry (2019)
    Purpose Urinary extracellular vesicles (uEVs) are a novel source of biomarkers. However, urinary Tamm-Horsfall Protein (THP; uromodulin) interferes with all vesicle isolation attempts, precipitates with normal urinary proteins, thus, representing an unwanted "contaminant" in urinary assays. Thus, the aim is to develop a simple method to manage THP efficiently. Experimental design The uEVs are isolated by hydrostatic filtration dialysis (HFD) and treated with a defined solution of urea to optimize release of uEVs from sample. Presence of uEVs is confirmed by transmission electron microscopy, Western blotting, and proteomic profiling in MS. Results Using HFD with urea treatment for uEV isolation reduces sample complexity to a great extent. The novel simplified uEV isolation protocol allows comprehensive vesicle proteomics analysis and should be part of any urine analytics to release all sample constituents from THP trap. Conclusions and clinical relevance The method brings a quick and easy protocol for THP management during uEV isolation, providing major benefits for comprehensive sample analytics.
  • Räsänen, Kati; Dang, Kien X.; Mustonen, Harri; Ho, Tho H.; Lintula, Susanna; Koistinen, Hannu; Stenman, Ulf-Håkan; Haglund, Caj; Stenman, Jakob (2018)
    The mitogen-activated protein kinase (MAPK) pathway plays a central role in colorectal cancers (CRC). In particular, BRAF V600E-mutant tumors, which represent around 10% of CRCs, are refractory to current therapies. Overexpression and secretion of serine peptidase inhibitor Kazal type 1 (SPINK1) are observed in around 50% of CRCs, and its serum level can be used as a biomarker for poor prognosis. Utilizing a recently developed extendable blocking probe assay, we analyzed the BRAF mutation status in a CRC patient cohort (N=571) using tissue-derived RNA as the starting material. From the same RNA samples, we measured the relative SPINK1 expression levels using a quantitative real-time PCR method. Expression of mutant BRAF V600E correlated with poor prognosis, as did low expression of SPINK1 mRNA. Further, BRAF V600E correlated negatively with SPINK1 levels. In order to investigate the effect of MAPK pathway-targeted therapies on SPINK1 secretion, we conducted invitro studies using both wild-type and V600E CRC cell lines. BRAF inhibitor vemurafenib, and subsequent MAPK pathway inhibitors trametinib and SCH772984, significantly increased SPINK1 secretion in V600E CRC cell lines Colo205 and HT-29 with a concomitant decrease in trypsin-1 and -2 secretion. Notably, no SPINK1 increase or trypsin-1 decrease was observed in BRAF wild-type CRC cell line Caco-2 in response to MAPK pathway inhibitors. In further mechanistic studies, we observed that only trametinib was able to diminish completely both MEK and ERK phosphorylation in the V600E CRC cells. Furthermore, the key regulator of integrated stress response, activating transcription factor 4 (ATF-4), was downregulated both at mRNA and at protein level in response to trametinib treatment. In conclusion, these data suggest that sustained inhibition of not only MAPK pathway activation, but also ATF-4 and trypsin, might be beneficial in the therapy of BRAF V600E-mutant CRC and that SPINK1 levels may serve as an indicator of therapy response.
  • Muroya, Susumu; Ueda, Shuji; Komatsu, Tomohiko; Miyakawa, Takuya; Ertbjerg, Per (2020)
    In the past decades, metabolomics has been used to comprehensively understand a variety of food materials for improvement and assessment of food quality. Farm animal skeletal muscles and meat are one of the major targets of metabolomics for the characterization of meat and the exploration of biomarkers in the production system. For identification of potential biomarkers to control meat quality, studies of animal muscles and meat with metabolomics (MEATabolomics) has been conducted in combination with analyses of meat quality traits, focusing on specific factors associated with animal genetic background and sensory scores, or conditions in feeding system and treatments of meat in the processes such as postmortem storage, processing, and hygiene control. Currently, most of MEATabolomics approaches combine separation techniques (gas or liquid chromatography, and capillary electrophoresis)-mass spectrometry (MS) or nuclear magnetic resonance (NMR) approaches with the downstream multivariate analyses, depending on the polarity and/or hydrophobicity of the targeted metabolites. Studies employing these approaches provide useful information to monitor meat quality traits efficiently and to understand the genetic background and production system of animals behind the meat quality. MEATabolomics is expected to improve the knowledge and methodologies in animal breeding and feeding, meat storage and processing, and prediction of meat quality.
  • Buzkova, Jana; Nikkanen, Joni; Ahola, Sofia; Hakonen, Anna H.; Sevastianova, Ksenia; Hovinen, Topi; Yki-Järvinen, Hannele; Pietiläinen, Kirsi H.; Lönnqvist, Tuula; Velagapudi, Vidya; Carroll, Christopher J.; Suomalainen, Anu (2018)
    Mitochondrial disorders (MDs) are inherited multi-organ diseases with variable phenotypes. Inclusion body myositis (IBM), a sporadic inflammatory muscle disease, also shows mitochondrial dysfunction. We investigated whether primary and secondary MDs modify metabolism to reveal pathogenic pathways and biomarkers. We investigated metabolomes of 25 mitochondrial myopathy or ataxias patients, 16 unaffected carriers, six IBM and 15 non-mitochondrial neuromuscular disease (NMD) patients and 30 matched controls. MD and IBM metabolomes clustered separately from controls and NMDs. MDs and IBM showed transsulfuration pathway changes; creatine and niacinamide depletion marked NMDs, IBM and infantile-onset spinocerebellar ataxia (IOSCA). Low blood and muscle arginine was specific for patients with m.3243A>G mutation. A four-metabolite blood multi-biomarker (sorbitol, alanine, myoinositol, cystathionine) distinguished primary MDs from others (76% sensitivity, 95% specificity). Our omics approach identified pathways currently used to treat NMDs and mitochondrial stroke-like episodes and proposes nicotinamide riboside in MDs and IBM, and creatine in IOSCA and IBM as novel treatment targets. The disease-specific metabolic fingerprints are valuable "multi-biomarkers" for diagnosis and promising tools for follow-up of disease progression and treatment effect.
  • Salmikangas, Marko Erkki Kristian (Helsingin yliopisto, 2020)
    Background Merkel Cell Carcinoma (MCC) is a rare neuroendocrine tumor that is associat-ed with old age and immunosuppressive condition. It has two distinct sub-groups differentiated with their Merkel Cell Polyomavirus (MCPyV) positivi-ty/negativity. While both groups are considered aggressive, the Merkel cell Pol-yomavirus negative group has significantly worse prognosis. Traditionally MCC cases have been diagnosed based on their physiological appearance and im-munohistochemical markers such as cytokeratin 20 and tumor transcription factor-1, which differentiate MCCs from small cell carcinomas. It still requires skilled personnel such as dermatologists and pathologists to identify MCCs. More precise and effective biomarkers are required to improve MCC diagnos-tics, to enhance patient survival and in the development of personalized medi-cine for MCC. Neurocan (NCAN) is a chondroitin sulphate proteoglycan that is found mainly in central nervous tissue in adults. The core protein of Neurocan is formed of 3 domains, G1 containing a single immunoglobulin domain, the glycosamino-glycan binding backbone and G3 domain containing regulatory protein-like sequences and epidermal growth factor/lectin-like domains. It is produced mainly by reactive astrocytes and its main function is to guide the growth of ax-ons and to participate in the formation of neural extracellular matrix. Neurocan is linked to inhibition of axonal regeneration and glial scarring in case of neu-ral injury. There are few mentions of Neurocan changes related to cancer out-side of the central nervous system, however, there is clear evidence of chon-droitin sulphate proteoglycan involvement in tumor invasiveness and potential-ly promotion of malignant tumor phenotype. Aim of the study and experimental design This thesis is a part of a project studying novel biomarkers and therapeutic tar-gets for MCC. The aim of the study was to identify a novel cancer specific gene (Neurocan) that would be either a potential biomarker or therapeutic target, and to set up the pipeline for further expanding the parent project. Neurocan was first identified from outlier gene detection methods applied to MCC sample series containing samples of 141 MCC patients. After this Neu-rocan expression levels were studied at protein level using immunohistochem-istry for MCC sample series. NCAN expression levels in MCC cell lines were investigated at mRNA and protein level with qPCR and Western blotting re-spectively. Functional studies of Neurocan such as an effect on cell prolifera-tion were performed with siRNA knockdown assays, and analyzed with West-ern blotting and qPCR. Results 144 FFPE samples in TMA (tissue microarray) format were stained for Neu-rocan protein expression; 31 samples expressed NCAN at low level, 60 at in-termediate level and 53 cases had high NCAN expression. The low NCAN ex-pression correlated with poor MCC specific survival (5-year survival 44%) when compared to intermediate and high expression groups (5-year survival 73% and 65% respectively). Kaplan-Meier survival analysis also implicated a signifi-cant difference in survival between the groups, p-value 0.044. NCAN expres-sion levels had a strong association with Merkel Cell Polyomavirus (MCPyV) status (Pearson Chi-square, p-value = 0.006) with 83% of high NCAN expres-sion cases being MCPyV positive, where as 55% of low NCAN expression cases were MCPyV negative. Cox proportional hazards model revealed that NCAN is unlikely to be an independent variable in patient survival. NCAN expression correlated with the MCPyV status of 9 tested MCC cell lines (Student’s t-test, p-value = 0.041). Protein level studies were inconclusive due to lack of specific antibodies and testing methods. 4 cell lines were tested for NCAN functionality in cell cultures. siRNA knock-down of NCAN did not affect the survival of MCC cell lines, however, it had a reducing effect on Large T-antigen expression of the MCPyV positive cell lines. Likewise, siRNA knockdown of Large T-antigen reduced the expression of NCAN mRNA in MCPyV positive cell lines. No such interactions were found in the MCPyV negative cell lines. siRNA knockdown of sT-antigen significantly reduced the growth of MCPyV positive WaGa cell line (Student’s t-test, p-value = 0.01). NCAN and large T-antigen targeting siRNAs had only a minor growth reducing effect on WaGa cell lines, and MKL1 cell line saw only minor growth reduction with all of the different siRNA treatments. These were not statistically significant findings. Whether Neurocan expression is directly controlled by MCPyV T-antigens, or whether the regulation is due to a signaling cascade of sorts, is still unknown.