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Študija angiogeneze na ravni proteinov in mRNA v plazmi in tkivu bolnic z rakom endometrija
ID Roškar, Luka (Author), ID Smrkolj, Špela (Mentor) More about this mentor... This link opens in a new window, ID Lanišnik Rižner, Tea (Comentor)

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Abstract
Rak endometrija (RE) je najpogostejši ginekološki rak v razvitih državah, pojavnost pa še narašča. Znano je, da angiogeneza, proces tvorbe novih žil, omogoča raku hitro rast in širitev v okolno tkivo. V zgodnjih fazah nastanka raka pride do sproščanja pro-angiogenih in zaviranja anti-angiogenih faktorjev (AF), kar predstavlja potencial za odkrivanje novih bioloških označevalcev za natančnejšo zgodnjo neinvazivno diagnozo in predoperativno stratifikacijo ter pravilno izbiro terapevtskih možnosti pri pacientkah z RE. Hkrati pa bi potrjevanje izražanja genov AF neposredno v tumorskem tkivu lahko izboljšalo poznavanje etiologije ter klasifikacije RE. Raziskovanje procesov angiogeneze pri RE smo razdelili na tri zaporedno povezane faze. Najprej smo v prospektivni monocentrični pilotni raziskavi, v katero je bilo vključenih 76 pacientk po menopavzi (38 pacientk z endometrioidnim RE in 38 kontrolnih pacientk z benignimi ginekološkimi obolenji), analizirali plazemske koncentracije 37 različnih AF ter ovrednotili diagnostični in prognostični potencial bioloških označevalcev raka endometrija. Koncentracije AF v predoperativnih vzorcih plazme so bile izmerjene s tehnologijo visokozmogljive ELISE Luminex xMAP?. Plazemske koncentracije sTie-2 in G-CSF so bile pri pacientkah z RE v primerjavi z osebami kontrolne skupine pomembno nižje, plazemske koncentracije leptina pa so bile pri pacientkah s RE pomembno višje kot v kontrolni skupini pacientk. Plazemske koncentracije nevropilina-1 so bile višje pri pacientkah s slabo diferenciranim RE v primerjavi z ostalimi pacientkami z RE ter kontrolno skupino pacientk. Koncentracije folistatina so se izkazale višje pri pacientkah z limfovaskularno invazijo, plazemske koncentracije IL-8 pa so bile bistveno višje pri pacientkah z metastazami. V fazi validacije smo nato analizirali plazmo 202 pacientk, od katerih je bilo 91 diagnosticiranih z RE in 111 z benigno ginekološko boleznijo. Z Luminex xMAP ? tehnologijo smo izmerili predoperativne koncentracije šestih, na podlagi pilotne raziskave izbranih AF: leptina, IL-8, sTie-2, folistatina, nevropilina-1 in G-CSF. Plazemske koncentracije leptina so bile pri pacientkah z ER pomembno višje kot pri kontrolnih pacientkah. Leptin je bil višji pri pacientkah z RE tipa 1, medtem ko je bil IL-8 višji pri RE tipa 2, zlasti pri slabo diferenciranem endometrioidnem RE. Plazemske koncentracije IL-8 so bile pri pacientkah z RE, pri katerih je bila prisotna limfovaskularna (LVI) ali miometrijska invazija (MI), pomembno višje. Zraven osnovnih statističnih metod smo z metodami strojnega učenja razvili diagnostične modele, ki temeljijo na koncentracijah testiranih AF. Med univariantnimi modeli je, tako v množici podatkov za trening, kot tudi v testni množici, dosegel najboljše rezultate model, ki temelji na leptinu. Kombinacija starosti, IL-8, leptina in G-CSF se je izkazala kot najpomembnejša skupina dejavnikov v multivariantnem modelu z ROC AUC 0,94 na trening- in 0,81 na testni množici. Model, ki uporablja kombinacijo vseh šestih AF, BMI in starosti, je dosegel ROC AUC 0,89 na obeh množicah, kar nakazuje na visoko sposobnost tega modela za napovedovanje tveganja za prisotnost RE. Raziskovanje angiogeneze pri RE smo nadaljevali na ravni izražanja genov za AF. Pregledali smo javno dostopne nabore podatkov v zbirkah The Cancer Genome Atlas (TCGA) in Clinical Proteomic Tumor Analysis Consortium (CPTAC) za izražanje genov in proteinov povezanih z angiogenezo ter za nadaljnjo validacijo izbrali devet genov z več kot 3-kratno razliko v izražanju genov in hkrati z več kot 2-kratno razliko v koncentraciji proteinov med tkivom raka endometrija (T) in okolnim nerakavim tkivom endometrija (TA). V nadaljnjo analizo smo vključili še šest genov AF, ki smo jih predhodno izbrali na podlagi rezultatov naših prejšnjih raziskav (CSF3, IL8, LEP, NRP1, TEK, FST). Skupaj smo tako analizirali 15 genov z uporabo metode qPCR na skupini 36 pacientk z RE. V naši klinični kohorti sta bila gena IL8 in LEP pomembno bolj izražena, CXCL12, ENPP2, FBLN5, FGF2, LYVE1, PDGFRB, SERPINF1, TIMP2, TIMP3, NRP1 in TEK pa pomembno manj izraženi v T tkivu v primerjavi s TA tkivom. V zgodnjih fazah in nižjih gradusih RE, ne pa tudi v napredovalih stadijih ali agresivnejših oblikah RE, so bili geni za AF različno izraženi med T tkivom in TA tkivom. Geni so bili različno izraženi le v endometrijskem tkivu pacientk brez invazije v miometrij preko polovice (DMI) ali LVI. Ugotovili smo močnejše soizražanje genov v T tkivu kot v TA tkivu; korelacije so bile še posebej močne kadar je bila prisotna LVI. Pri ženskah po menopavzi z RE smo odkrili širšo vključenost genov, povezanih z angiogenezo, kot pri pacientkah v reproduktivni dobi. Nato smo z združitvijo podatkov iz naše raziskave ter TCGA razvili metodo modeliranja s strojnim učenjem za oblikovanje prognostičnega modela pri RE. Ustvarili smo prognostični model, ki razlikuje med RE nizkega in visokega gradusa na podlagi izražanja genov v tumorskem tkivu RE. Glede na naše rezultate je merjenje plazemskih koncentracij angiogenih faktorjev lahko pomembno dopolnilno diagnostično orodje za zgodnje odkrivanje in prognostično karakterizacijo RE. Naši podatki kažejo, da angiogenezo pri RE spodbuja predvsem zmanjšano izražanje genov antiangiogenih dejavnikov. Pri RE s prognostično manj ugodnimi značilnostmi je uravnavanje genov AF spremenjena tako v T tkivu kot v morfološko normalnem okolnem endometrijskem tkivu. Ugotovitve naših raziskav kažejo, da bi lahko plazemske ravni 6 različnih AF služile kot obetavni biološki označevalci ter diagnostično in prognostično orodje za zgodnje odkrivanje in karakterizacijo RE, zlasti, ko so vključeni v statistični model strojnega učenja. Ob tem ugotavljamo, da angiogenezo pri RE spodbuja predvsem zmanjšano izražanje genov anti-antiangiogenih molekul. Razultati nakazujejo spremenjeno izražanje AF ne samo v tumorskem ampak tudi v morfološko normalnem okolnem tkivu ob prisotnosti prognostično slabših kliničnih značilnostih kot sta LVI in MI. Za vzpostavitev natančnejšega diagnostičnega in prognostičnega modela s pomočjo strojnega učenja, ki bi upošteval izražanje genov AF v tkivu EC, je potrebna nadaljnja večja multicentrična raziskava.

Language:Slovenian
Keywords:biološki označevalci, angiogeneza, rak endometrija, angiogeni faktorji, Tie-2, G-CSF, leptin, IL-8, strojno učenje, izražanje genov
Work type:Doctoral dissertation
Organization:MF - Faculty of Medicine
Year:2023
PID:20.500.12556/RUL-152055 This link opens in a new window
Publication date in RUL:29.10.2023
Views:636
Downloads:95
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Secondary language

Language:English
Title:Study of angiogenesis-related proteins and mRNA expression in plasma and tissue of endometrial cancer patients
Abstract:
Endometrial cancer (EC) is the most frequent gynaecological cancer in developed countries, with its rates increasing. Its fast growth and spread are enabled by the angiogenic switch in the early stages of cancerogenesis through the release of pro-angiogenic and suppression of anti-angiogenic factors (AFs). Therefore, screening patients’ plasma biomarkers might enable a more precise diagnosis of EC and a tailored treatment approach. Furthermore, confirming AF gene expression directly in the tumour tissue can generate new knowledge on cancerogenesis and help identify biomarkers for the diagnosis and prognosis of EC. In our study, the investigation of angiogenesis in EC was divided into three sequentially related phases. Our first prospective case-control monocentric pilot study included 76 postmenopausal women (38 endometrioid EC patients and 38 control patients with benign gynaecological conditions), and 37 angiogenic factors (AFs) were investigated as potential biomarkers for EC. AF concentrations in pre-operative plasma samples were measured using Luminex xMAP〢 multiplexing technology. The plasma levels of sTie-2 and G-CSF were significantly lower in EC compared to control patients, whereas the plasma levels of leptin were significantly higher in EC patients. Neuropilin-1 plasma levels were significantly higher in patients with type 2 EC (grade 3) than those with lower-grade cancer or controls. Follistatin levels were significantly higher in patients with lymphovascular invasion, and IL-8 plasma levels were significantly higher in patients with metastases. In the validation study, we analysed 202 patients, of whom 91 were diagnosed with EC, and 111 were control patients with benign gynaecological disease. We used Luminex xMAP〢 multiplexing technology to measure the pre-operative plasma concentrations of six previously selected angiogenic factors – leptin, IL-8, sTie-2, follistatin, neuropilin-1, and G-CSF. The plasma levels of leptin were significantly higher in EC patients than in control patients. Leptin was higher in type 1 EC patients, and IL-8 was higher in type 2 EC, particularly in poorly differentiated endometrioid EC grade 3. In addition, IL-8 plasma levels were significantly higher in EC patients with lymphovascular or myometrial invasion. Besides basic statistical methods, we used a machine-learning algorithm to create a robust diagnostic model based on the plasma concentration of tested angiogenic factors. Among univariate models, the model based on leptin reached the best results on both training and test datasets. A combination of age, IL-8, leptin and G-CSF was determined as the essential feature for the multivariate model, with ROC AUC 0.94 on training and 0.81 on the test dataset. The model utilizing a combination of all six AFs, BMI and age reached a ROC AUC of 0.89 on both the training and test dataset, strongly indicating the capability for predicting the risk of EC even on unseen data. Additionally, we evaluated publicly available datasets for the expression of angiogenesis-associated genes and proteins in EC tissues (T) compared to tumour-adjacent control tissue (TA). Nine genes with more than a 3-fold significant difference in gene expression in concert with more than a 2-fold significant difference in protein levels between T and TA tissue, together with six AF genes preselected in our previous plasma-based research (CSF3, IL8, LEP, NRP1, TEK, FST), were selected for validation on EC tissue, using the qPCR method on a cohort of 36 EC patients. By combining TCGA data and data from our study, we applied machine learning modelling to create the EC grade prediction model. In our clinical cohort, IL8 and LEP were significantly upregulated, and CXCL12, ENPP2, FBLN5, FGF2, LYVE1, PDGFRB, SERPINF1, TIMP2, TIMP3, NRP1 and TEK were significantly downregulated in T vs TA tissue. In early stages and lower grades of EC, but not in more advanced or aggressive forms of EC, genes for AFs were differentially expressed between T and TA tissue. Genes were differentially expressed only in endometrial tissue from patients without deep myometrial (DMI) or lymphovascular invasion (LVI). We identified stronger gene co-expressions within T than TA tissue; correlations were particularly strong when LVI was present. In addition, we detected broader angiogenesis-related gene involvement in postmenopausal women with EC than in women of reproductive age. Finally, machine learning modelling created a relatively robust EC model based on the T gene expressions, differentiating between low and high-grade EC. According to our results, measuring plasma concentrations of AFs could represent an important supplementary diagnostic tool for early detection and prognostic characterization of EC, which could guide the decision-making regarding the extent of treatment. Our data suggest that angiogenesis in EC is promoted mainly by decreased gene expression of anti-angiogenic factors. In EC with prognostically less favourable characteristics, the regulation of AF genes is altered in T tissue as well as in morphologically normal TA tissue. The findings from our studies suggest that the plasma levels of 6 AFs could serve as promising biomarkers, offering a valuable diagnostic and prognostic tool for early detection and characterization of EC. Particularly when incorporated into a machine learning statistical algorithm model, these AFs show great potential. Additionally, our data highlights that the regulation of angiogenesis-related genes in EC, specifically in tissues surrounding the endometrium, also plays a role in the prognosis of the disease. To establish a more precise diagnostic and prognostic machine learning model based on AF gene expression in EC tissue, further research collaboration among multiple centers is necessary.

Keywords:biomarkers, angiogenesis, endometrial cancer, angiogenic factors, Tie-2, G-CSF, leptin, IL-8, machine learning, gene expression

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