Bridging the gap between microarray technology and routine clinical diagnostics: a Random Forest approach to the gene expression profile dimensionality reduction

Uvod: Analiza genske ekspresije zasnovana na mikropostrojima je tijekom proteklog desetljeća prepoznata kao koristan alat od strane znanstvene zajednice, ali nije ušla u rutinsku dijagnostičku primjenu. Kako je skupa i podložna značajnim eksperimentalnim varijacijama, na trenutnom tehnološkom stupnju razvoja ta tehnologija nije prikladna za rutinske kliničko-dijagnostičke primjene. U svrhu premošćivanja jaza između mogućnosti navedene tehnologije i potreba kliničke dijagnostike razvijeni su različiti računalni alati za smanjenje dimenzionalnosti. Njihova osnovna svrha je odabir malog skupa kandidata za biomarkere iz ogromnog skupa sadržanog u profilima genske ekspresije prikladnog za rutinsko postavljanje dijagnoze. Cilj: Slučajna šuma (engl. Random Forest, RF) se nametnula kao pouzdan pretkazatelj. Ipak, njene su mogućnosti u odabiru relevantnih gena privukle manje pažnje. Cilj ove studije je evaluacija prikladnosti na RF-u zasnovanoga odabira biomarkera iz skupova genskih profila. Tri takva skupa, preuzeta iz literature, prikupljena tijekom manjih kliničkih pokusa izabrana su u navedenu svrhu. Rezultati: Dobiveni rezultati ukazuju da RF može lako identificirati dobre uni-varijatne klasifikatore, tj. pojedinačne biomarkere kada je složenost skupa mala. Za nešto složenije probleme pouzdani dvodimenzionalni klasifikator može se također pronaći. Ipak, ako je odnos između dijagnoze/prognoze i profila genske ekspresije vrlo složen ili ako je skup premalen, na RF-u zasnovano smanjenje dimenzionalnosti ne omogućava odabir pouzdanog skupa kandidata za biomarkere. Zaključci: Unutar ograničenja zadanih složenošću skupa RF predstavlja prikladan alat za izbor kandidata za biomarkere.ntroduction: Although recognized as a valuable tool by scientific community, microarray based gene expression profiling has not accessed routine diagnostic application during the last decade. Since this approach is expensive and prone to substantial experimental variation, it is not suited for routine clinical diagnostic purposes at the current state of technology. In order to bridge that gap, different computational dimensionality reduction tools have been developed. The principle of their application is selection of a limited set of biomarker candidates from huge gene expression profiles appropriate for routine diagnostic assessment. Aim: Random forest (RF) has been established as a reliable predictor. However, its relevant gene selection capabilities gained less attention. The aim of this study was to evaluate suitability of RF for biomarker selection from gene expression profile datasets. Three datasets taken from literature, obtained during small-scale clinical experiments, were chosen for that purpose. Results: The results obtained show that RF could easily identify good uni-variate classifiers, i.e. single biomarkers when the problem at hand is of low complexity. For more complex problem a reliable two-dimensional classifier candidate could be also found by this approach. However, when the relationship between diagnosis/prognosis and gene expression profiling results are highly complex or the dataset is too small, RF-based dimensionality reduction fails to select a reliable set of biomarker candidates. Conclusions: Within dataset complexity limitations, RF represents an appropriate tool for biomarker candidate selection

Bridging the gap between microarray technology and routine clinical diagnostics: a Random Forest approach to the gene expression profile dimensionality reduction

Uvod: Analiza genske ekspresije zasnovana na mikropostrojima je tijekom proteklog desetljeća prepoznata kao koristan alat od strane znanstvene zajednice, ali nije ušla u rutinsku dijagnostičku primjenu. Kako je skupa i podložna značajnim eksperimentalnim varijacijama, na trenutnom tehnološkom stupnju razvoja ta tehnologija nije prikladna za rutinske kliničko-dijagnostičke primjene. U svrhu premošćivanja jaza između mogućnosti navedene tehnologije i potreba kliničke dijagnostike razvijeni su različiti računalni alati za smanjenje dimenzionalnosti. Njihova osnovna svrha je odabir malog skupa kandidata za biomarkere iz ogromnog skupa sadržanog u profilima genske ekspresije prikladnog za rutinsko postavljanje dijagnoze. Cilj: Slučajna šuma (engl. Random Forest, RF) se nametnula kao pouzdan pretkazatelj. Ipak, njene su mogućnosti u odabiru relevantnih gena privukle manje pažnje. Cilj ove studije je evaluacija prikladnosti na RF-u zasnovanoga odabira biomarkera iz skupova genskih profila. Tri takva skupa, preuzeta iz literature, prikupljena tijekom manjih kliničkih pokusa izabrana su u navedenu svrhu. Rezultati: Dobiveni rezultati ukazuju da RF može lako identificirati dobre uni-varijatne klasifikatore, tj. pojedinačne biomarkere kada je složenost skupa mala. Za nešto složenije probleme pouzdani dvodimenzionalni klasifikator može se također pronaći. Ipak, ako je odnos između dijagnoze/prognoze i profila genske ekspresije vrlo složen ili ako je skup premalen, na RF-u zasnovano smanjenje dimenzionalnosti ne omogućava odabir pouzdanog skupa kandidata za biomarkere. Zaključci: Unutar ograničenja zadanih složenošću skupa RF predstavlja prikladan alat za izbor kandidata za biomarkere.ntroduction: Although recognized as a valuable tool by scientific community, microarray based gene expression profiling has not accessed routine diagnostic application during the last decade. Since this approach is expensive and prone to substantial experimental variation, it is not suited for routine clinical diagnostic purposes at the current state of technology. In order to bridge that gap, different computational dimensionality reduction tools have been developed. The principle of their application is selection of a limited set of biomarker candidates from huge gene expression profiles appropriate for routine diagnostic assessment. Aim: Random forest (RF) has been established as a reliable predictor. However, its relevant gene selection capabilities gained less attention. The aim of this study was to evaluate suitability of RF for biomarker selection from gene expression profile datasets. Three datasets taken from literature, obtained during small-scale clinical experiments, were chosen for that purpose. Results: The results obtained show that RF could easily identify good uni-variate classifiers, i.e. single biomarkers when the problem at hand is of low complexity. For more complex problem a reliable two-dimensional classifier candidate could be also found by this approach. However, when the relationship between diagnosis/prognosis and gene expression profiling results are highly complex or the dataset is too small, RF-based dimensionality reduction fails to select a reliable set of biomarker candidates. Conclusions: Within dataset complexity limitations, RF represents an appropriate tool for biomarker candidate selection

Carbohydrate sulfotransferases: a review of emerging diagnostic and prognostic applications

Carbohydrate sulfotransferases (CHST) catalyse the biosynthesis of proteoglycans that enable physical interactions and signalling between different neighbouring cells in physiological and pathological states. The study aim was to provide an overview of emerging diagnostic and prognostic applications of CHST. PubMed database search was conducted using the keywords “carbohydrate sulfotransferase” together with appropriate inclusion and exclusion criteria, whereby 41 publications were selected. Additionally, 40 records on CHST genetic and biochemical properties were hand-picked from UniProt, GeneCards, InterPro, and neXtProt databases. Carbohydrate sulfotransferases have been applied mainly in diagnostics of connective tissue disorders, cancer and inflammations. The lack of CHST activity was found in congenital connective tissue disorders while CHST overexpression was detected in different malignancies. Mutations of CHST3 gene cause skeletal dysplasia, chondrodysplasia, and autosomal recessive multiple joint dislocations while increased tissue expression of CHST11, CHST12 and CHST15 is an unfavourable prognostic factor in ovarian cancer, glioblastoma and pancreatic cancer, respectively. Recently, CHST11 and CHST15 overexpression in the vascular smooth muscle cells was linked to the severe lung pathology in COVID-19 patients. Promising CHST diagnostic and prognostic applications have been described but larger clinical studies and robust analytical procedures are required for the more reliable diagnostic performance estimations

Pathologic patterns of interleukin 10 expression – A review

Interleukin 10 (IL-10) is important pleiotropic immunoregulatory cytokine which gene is located on chromosome 1 at 1q31-32. There are many genetic variants of IL-10 gene. However, the most studied are two dinucleotide repeats (microsatellites), IL10.G and IL10.R, located 1.2 kb and 4 kb upstream of the transcription start site and three single nucleotide polymorphisms (SNPs) -1082(G/A), -819(C/T) and -592(C/A). A large number of studies have shown that IL-10 gene polymorphisms are associated with different diseases and play an important role in pathophysiology and clinical course of these diseases. This review summarizes published literature knowledge about the association of IL-10 polymorphisms and expression patterns with asthma, systemic lupus erythematosus, psoriasis, inflammatory bowel disease, rheumatoid arthritis, tuberculosis and some neoplasm

Homozygous form of hereditary hemochromatosis in a patient with beta-thalassemia minor: case report

Uvod: Dijagnostički pristup bolesniku koji istodobno boluje od nasljedne hemokromatoze i beta-talasemije može biti dosta složen zbog činjenice da teži oblici beta-talasemije sami po sebi mogu imati za posljedicu hemokromatozu. S druge strane, i najlakši oblik beta-talasemije može dovesti do ozbiljnih manifestacija hemokromatoze u bolesnika s heterozigotnim oblikom HFE polimorfizama. Ova stanja, kao i HFE polimorfizmi naslijeđeni u homozigotnom obliku kao rizični čimbenici za razvoj hemokromatoze mogu imati za posljedicu cirozu jetre i hepatocelularni karcinom pa pravodobno prepoznavanje navedenih stanja ima presudno značenje za dužinu i kvalitetu bolesnikova života. Metode: Za prikaz slučaja izabran je bolesnik primljen na Kliniku za zarazne bolesti Kliničke bolnice Osijek s febrilitetom, hepatosplenomegalijom i neurološkim simptomima. Kod prijma su učinjene osnovne laboratorijske pretrage te ultrazvučni pregled abdomena i snimanje glave magnetskom rezonancijom. Naknadno je provedena biopsija jetre, elektroforeza hemoglobina te određivanje koncentracije haptoglobina i utvrđivanje Cys282Tyr polimorfizma HFE gena. Rezultati: Anamnestički podaci i rezultati rutinske laboratorijske obrade su ukazali na mogućnost da bolesnik boluje od beta-talasemije. Proširenom laboratorijskom obradom je dijagnosticirana pigmentna ciroza-hemokromatoza, a potvrđena je dijagnoza beta-talasemije minor. Odgovarajući moleularno-dijagnostički postupak je dokazao prisutnost homozigotnog oblika nasljedne hemokromatoze. Zaključak: Određivanje koncentracije feritina i zasićenje transferina željezom, elektroforeza hemoglobina i utvrđivanje polimorfizma Cys282Tyr HFE gena pokazali su se ključnim čimbenicima za relativno brzo postavljanje ispravne dijagnoze u prikazanom slučaju istodobnog nasljeđivanja beta-talasemije minor i homozigotnog oblika nasljedne hemokromatoze. Homozigotni oblik nasljedne hemokromatoze uz beta-talasemiju minor objašnjava težinu simptoma prisutnih kod bolesnika u vrijeme hospitalizacije.Background: Diagnostic approach to the simultaneous inheritance of beta-thalassemia and hereditary hemochromatosis might be quite complex due to the fact that severe beta-thalassemia itself may lead to hemochromatosis. On the other hand, beta-thalassemia minor accompanied by some heterozygous form of HFE polymorphism may also lead to the disease manifestation. These conditions as well as the homozygous forms of HFE polymorphisms are hemochromatosis risk factors that may lead to liver cirrhosis and hepatocellular carcinoma. Therefore, early diagnosis is crucial for patient quality of life and life expectancy. Methods: A febrile patient admitted to Department of Infectious Diseases, Osijek University Hospital, with hepatosplenomegaly and some neurological symptoms has been chosen for this case report. Basic laboratory tests as well as ultrasound examination of the abdomen and magnetic resonance imaging of the head were performed shortly upon admission. Liver biopsy, hemoglobin electrophoresis, haptoglobin concentration and Cys282Tyr polymorphism determination were subsequently obtained. Results: History data and laboratory findings suggested the diagnosis of beta-thalassemia. Extended laboratory work-up pointed to the diagnosis of pigment cirrhosis-hemochromatosis, and verified the diagnosis of beta-thalassemia minor. Appropriate molecular diagnostic procedure indicated the homozygous form of hereditary hemochromatosis. Conclusions: In this case of homozygous hereditary hemochromatosis and beta-thalassemia minor coinheritance, serum ferritin concentration, tran-sferrin saturation, hemoglobin electrophoresis and HFE gene Cys282Tyr polymorphism analysis proved to be crucial for the relatively fast establishment of accurate diagnosis. Recognition of the homozygous form of hemochromatosis in association with beta-thalassemia minor explained the complexity and severity of the disease presentation

Veza poznavanja nogometa i geografskog znanja maturanata Gimnazije Antuna Gustava Matoša u Samoboru

Geografija i nogomet dva su usko povezana pojma i učenjem o jednome često naučimo nešto i o drugome. Prema tome, osobe koje prate nogomet raspolažu s više geografskog, pretežno činjeničnog znanja od osoba koje nogomet ne prate. Hipoteza ovog rada je da osoba koja prati nogomet, samim poznavanjem nogometnih klubova i liga u kojim se ti klubovi natječu, posjeduje razinu geografskog znanja kakvu osobe koje ne prate nogomet ne posjeduju. Anketnim upitnikom dokazano je postojanje srednje jake pozitivne korelacije između geografskog i nogometnog znanja, čime je potvrđena hipoteza ovog rada

Vitamin D Deficiency Among Medical Students in Osijek, Croatia

Aim: This study aimed to evaluate serum levels of 25-OH D3 (calcidiol) among students of the Faculty of Medicine Osijek, Croatia, thereby determining to what extent vitamin D deficiency is present. Methods: The present cross-sectional analysis was based on data collected from 60 participants. Blood sampling was done in March 2021. Concentrations of 25-OH D3 were measured using LC/MS-MS procedure on Shimadzu LCMS 8050 and RECIPE kit for serum levels of 25-OH-D3. Results: The study was conducted on a sample of 60 respondents aged 19 to 28, of whom 16 were men and 44 were women. All subjects had a 25-OH D3 deficiency (0.05). Conclusion: Vitamin D deficiency was detected in all subjects. In addition to the results of several other studies conducted worldwide that evaluated vitamin D status among medical students, this study further highlights the problem affecting this student subgroup

Veza poznavanja nogometa i geografskog znanja maturanata Gimnazije Antuna Gustava Matoša u Samoboru

Geografija i nogomet dva su usko povezana pojma i učenjem o jednome često naučimo nešto i o drugome. Prema tome, osobe koje prate nogomet raspolažu s više geografskog, pretežno činjeničnog znanja od osoba koje nogomet ne prate. Hipoteza ovog rada je da osoba koja prati nogomet, samim poznavanjem nogometnih klubova i liga u kojim se ti klubovi natječu, posjeduje razinu geografskog znanja kakvu osobe koje ne prate nogomet ne posjeduju. Anketnim upitnikom dokazano je postojanje srednje jake pozitivne korelacije između geografskog i nogometnog znanja, čime je potvrđena hipoteza ovog rada

THE INFLUENCE OF WATER MACROPHYTES ON THE QUANTITY OF OXYGEN IN CARP PONDS\u27 WATER

Istraživanja djelovanja zaraštenosti šaranskih ribnjaka emerznim makrofitima provedena su a ribnjacima ribnjačarstva D. Miholjac tijekom Ijetnih mjeseci uzgojne sezone god. 1988. i 1989. Istraživanja su provedena u šest ribnjaka, od kojih se a četiri ribnjaka (1, 2, 3 i 4) uzgajao riblji mlad, a u dva ribnjaka (5 i 6) konzumna riba. Obraštenost pojedinih ribnjaka emerznim makrofitima bila je 40 do 70 % površine ribnjaka, a prevladavala je vrsta Nymphoides peltata. Rezultate istraživanja prikazuju tabl. 3. i 4. te sl. 1. Sadržaj kisika a vodi nezaraštenih površina varirao je unutar amplitude od 2,72 mgl-1 do 11,20 mgl-1, što upućuje na povremenu nepoželjnu razinu s gledišta potreba za normalnom prehranom i rast uzgajanih riba. U dijelovima ribnjaka intenzivno zaraštenim emerznim biljem količina se kisika znatno smanjivala uz varijacije unutar amplitude od 1,28 mgl-1 do 7,84 mgl-1 odnosno a svim ribnjacima bila je od 0,32 do 3,84 mgl-1 (9 - 54 %) niža od količine kisika u vodi slobodnih, nezaraštenih dijelova ribnjaka. Ta je razlika bila i statistički opravdana (P < 0,05). Rezultati ovih istraživanja upućuju na znatan negativni utjecaj emerznih makrofita a šaranskim ribnjacima. Ovisno o intenzitetu obraštenosti ribnjaka, smanjuje se i količina kisika a vodi, što smanjuje mogućnost normalne prehrane riba dodatnom hranom. Nedovoljna količina kisika a vodi rezultira slabijom iskorištenošću dodatne riblje hrane, manjim ukupnim prirastima riba i povećanim hranidbenim koeficijentom. Stoga zaključujemo da je očita važnost suzbijanja prekomjerna razvoja vodnih makrofita, ekološke skupine emerznih biljaka, a šaranskim ribnjacima.Research on the influence of emersed macrophytes in carp ponds in fish-farm D. Miholjac was carried on during the summer months of 1988 and 1989. Six carp ponds were under research: in ponds number 1, 2, 3 and 4, the fingerlings were cultured and in the ponds number 5 and 6, marketable fish. Some ponds had 40 - 70% of their area covered by emerged macrophytes, Nymphoides peltata being the dominant species. The results are presented in tables 3 and 4 and on figure 1. The quantity of oxygen in the water of pond areas without emersed macrophytes varied between 2.72 mgl-1 and 11,20 mgl-1 indicating temporary insufficiency as far as requirements for normal growth were concerned. In extremely overgrown areas of the ponds, the quantity of oxygen decreased significantly varying within an amplitude from 1.28 mgl-1 to 7,84 mgl-1. As opposed to pond areas free of weeds, the quantity of oxygen was 9 - 54% lower (from 0.32 mgl-1 to 3.84 mgl-1) in overgrown parts of pond areas. The fact was even significant statistically (p < 0.05). The results indicate significantly negative influence of emersed macrophytes on the carp ponds. The oxygen level in water becomes lower as the overgrowth of the pond area becomes more extensive. That makes the possibility of otherwise normal fish feeding by additional food less convenient. Without the additional food, total fish mass increments are lower, and the food coefficient becomes higher. All of this shows the importance of reducing the overdevelopment of emersed macrophytes in the carp ponds. Therefore, the uprooting of emersed macrophytes from carp pond areas in of utmost importance