Development of novel loxl1 genotyping method and evaluation of loxl1, apoe and mthfr polymorhisms in exfoliation syndrome/glaucoma (xfs/xfg) in a Greek population

PurposePseudoexfoliation syndrome (PXFS) is a late-onset and complex disorder involving a combination of genetic and non-genetic factors in its etiopathogenesis. PXFS is one of the most commoncauses of glaucoma worldwide. In the Greek population of Epirus, PXFS and pseudoexfoliation glaucoma (PXFG) occur at a high prevalence. In this study, we validate a novel genotyping LOXL1method, investigate the previously reported association of LOXL1 with PXFS/PXFG, and evaluateAPOE and MTHFR polymorphisms as genetic risk factors for both these conditions in ourpopulation. MethodsBlood samples were collected from 82 patients with PXFG, 69 patients with PXFS, 52 patients withprimary open-angle glaucoma (POAG) and 107 controls. APOE and MTHFR 677C>T genotypingwas performed from extracted genomic DNA by established methods. A novel methodology of real-time PCR and melting curve analysis was developed and validated in order to accurately genotypethe LOXL1 G153D and R141L polymorphisms by using two different fluorescent channels of the LightCycler instrument (Roche) examining each SNP separately.ResultsNo significant differences were observed for the APOE and MTHFR polymorphisms betweenPXFS, PXFG and control subjects. The APOE ε2 allele appears to be associated with elevated risk of POAG in our population. Our novel LOXL1 genotyping method was easy to perform, fast and accurate. A statistically significant association was found for LOXL1 gene with PXFS/PXFG in this Greek population. The association of PXFS and PXFG with G153D appeared to be less powerful in this population (PXFS: OR=2.162, p=0.039, XFG: OR=2.794, p=0.002) compared to otherpopulations and as for R141L, the association was proven only with PXFG (OR=3.592, p<0.001). None of the two LOXL1 SNPs was significantly associated with POAG.Conclusions We confirmed the association between LOXL1 and PXFS/PXFG, while the APOE and MTHFRpolymorphisms are not significant risk factors for the development of PXFS/PXFG in our population of patients from Epirus (Greece). In our population, we suggest that the R141L LOXL1 maycontribute to XFG onset independently rather than through IOP elevation and subsequent glaucoma.ΣκοπόςΤο ψευδοαποφολιδωτικό σύνδρομο (Ψ/Α.Σ) αποτελεί μια σύνθετη πάθηση, με όψιμη έναρξη εμφάνισηστην οποία εμπλέκονται πολλαπλά γονίδια και/ή περιβαλλοντικοί παράγοντες. Το Ψ/Α.Σ αποτελεί τoπιο συχνά προσδιορισμένο αίτιο χρόνιου γλαυκώματος ανοικτής γωνίας. Στον ελληνικό πληθυσμό τηςΗπείρου, το Ψ/Α.Σ και το ψευδοαποφολιδωτικό γλαύκωμα (Ψ/Α.Γ) απαντώνται σε υψηλή συχνότητα.Στην παρούσα μελέτη, αναπτύξαμε μία αξιόπιστη μεθοδολογία για τη γονοτύπωση του γονιδίουLOXL1, διερευνήσαμε την αναφερόμενη σύνδεση του LOXL1 με το Ψ/Α.Σ-Ψ/Α.Γ και εκτιμήσαμε τηνσυμβολή των πολυμορφισμών APOE και MTHFR ως γενετικοί δείκτες κινδύνου και στις δύοκαταστάσεις στον πληθυσμό μας.ΜέθοδοςΣυλλέχθηκαν δείγματα αίματος από 82 ασθενείς με Ψ/Α.Γ, 69 ασθενείς με Ψ/Α.Σ, 52 ασθενείς με πρωτοπαθές γλαύκωμα ανοικτής γωνίας (ΠΓΑΓ) και 107 άτομα ομάδας ελέγχου. Η γονοτύπωση τωνπολυμορφισμών του APOE και MTHFR C677T πραγματοποιήθηκε με εξακριβωμένες μεθόδους από τογενωμικό DNA που εξήχθη. Για τη γονοτύπωση δύο γνωστών σημειακών πολυμορφισμών (G153D καιR141L) του LOXL1 αναπτύχθηκε και βελτιστοποιήθηκε μεθοδολογία PCR πραγματικού χρόνου καιανάλυση καμπύλων τήξης για τους προαναφερθέντες πολυμορφισμούς του γονιδίου LOXL1 χρησιμοποιώντας δύο διαφορετικά κανάλια του οργάνου LightCycler (Roche), εξετάζοντας ξεχωριστάκάθε πολυμορφισμό.ΑποτελεσματαΔεν παρατηρήθηκαν στατιστικά σημαντικές διαφορές για τους πολυμορφισμούς του APOE και MTHFRμεταξύ Ψ/Α.Σ, Ψ/Α.Γ και ομάδας ελέγχου. Το Ε2 αλλήλιο του APOE φάνηκε να συνδέεται με αυξημένοκίνδυνο για ΠΓΑΓ στον υπό μελέτη πληθυσμό. H μεθοδολογία για το LOXL1 ήταν ταχεία και αξιόπιστη,επιδεικνύοντας καλή απόδοση και επαναληψιμότητα στην ποσοτικοποίηση και αξιοπιστία στηγονοτύπωση. Από τα αποτελέσματα επιβεβαιώνεται η σύνδεση του LOXL1 με το Ψ/Α.Σ-Ψ/Α.Γ σεΕλληνικό πληθυσμό. Η σύνδεση του Ψ/Α.Σ-Ψ/Α.Γ με τον G153D φάνηκε να είναι λιγότερο ισχυρή στονπληθυσμό που μελετήθηκε (Ψ/Α.Σ: OR=2,162, p=0,039, Ψ/Α.Γ: OR=2,794, p=0,002) σε σχέση μεάλλους πληθυσμούς σε διάφορες μελέτες. Ενώ για τον πολυμορφισμό R141L η σύνδεση αποδείχθηκεμόνο για το Ψ/Α.Γ (OR=3,529, p<0,001). Δεν προέκυψε σύνδεση του ΠΓΑΓ με κανένας από τους δύο πολυμορφισμούς του LOXL1.ΣυμπεράσματαΕπιβεβαιώσαμε την σύνδεση του LOXL1 με το Ψ/Α.Σ-Ψ/Α.Γ, ενώ οι πολυμορφισμοί του APOE καιMTHFR δεν αποτελούν σημαντικό παράγοντα κινδύνου για την ανάπτυξη Ψ/Α.Σ-Ψ/Α.Γ στον ελληνικόπληθυσμό από την Ήπειρο. Στον πληθυσμό μας, προτείνουμε ότι ο R141L μπορεί να συμβάλλει στηνεκδήλωση Ψ/Α.Γ ως ανεξάρτητος παράγοντας κινδύνου και όχι απαραιτήτως μέσω του Ψ/Α.

Explainable Machine Learning Models for Identification of Food-Related Lifestyle Factors in Chicken Meat Consumption Case in Northern Greece

A consumer’s decision-making process regarding the purchase of chicken meat is a multifaceted one, influenced by various food-related, personal, and environmental factors that interact with one another. The mediating effect of food lifestyle that bridges the gap between consumer food values and the environment, further shapes consumer behavior towards meat purchase and consumption. This research introduces the concept of Food-Related Lifestyle (FRL) and aims to identify and explain the factors associated with chicken meat consumption in Northern Greece using a machine learning pipeline. To achieve this, the Boruta algorithm and four widely recognized classifiers were employed, achieving a binary classification accuracy of up to 78.26%. The study primarily focuses on determining the items from the FRL tool that carry significant weight in the classification output, thereby providing valuable insights. Additionally, the research aims to interpret the significance of these selected factors in the decision-making process using the SHAP model. Specifically, it turns out that the freshness, safety, and nutritional value of chicken meat are essential considerations for consumers in their eating habits. Additionally, external factors like health crises and price fluctuations can have a significant impact on consumer choices related to chicken meat consumption. The findings contribute to a more nuanced understanding of consumer preferences, enabling the food industry to align its offerings and marketing efforts with consumer needs and desires. Ultimately, this work demonstrates the potential of AI in shaping the future of the food industry and informs strategies for effective decision-making

Development of novel LOXL1 genotyping method and evaluation of LOXL1, APOE and MTHFR polymorphisms in exfoliation syndrome/glaucoma in a Greek population

PURPOSE: In the Greek population of Epirus, exfoliation syndrome (XFS) and exfoliation glaucoma (XFG) occur at a high prevalence. In this study, we validate a novel lysyl oxidase-like 1 (LOXL1) genotyping method, investigate the previously reported association of LOXL1 with XFS/XFG, and evaluate apolipoprotein E (APOE) and methylenetetrahydrofolate reductase (MTHFR) polymorphisms as genetic risk factors for both conditions in our population. METHODS: Blood samples were collected from 82 patients with XFG, 69 patients with XFS, 52 patients with primary open-angle glaucoma (POAG), and 107 controls. APOE and MTHFR 677C>T genotyping was performed from extracted genomic DNA with established methods. A novel methodology of real-time PCR and melting curve analysis was developed and validated to accurately genotype the LOXL1 G153D and R141L polymorphisms by using two different fluorescent channels of the LightCycler instrument (Roche) examining each SNP separately. RESULTS: No significant differences were observed for the APOE and MTHFR polymorphisms between the patients with XFS, the patients with XFG, and the control subjects. The APOE ε2 allele appears to be associated with elevated risk of POAG in our population. Our novel LOXL1 genotyping method was easy to perform, fast, and accurate. A statistically significant association was found for the LOXL1 gene with XFS/XFG in this Greek population. The association of XFS and XFG with G153D appeared to be less powerful in this population (XFS: odds ratio [OR]=2.162, p=0.039, XFG: OR=2.794, p=0.002) compared to other populations, and for R141L, the association was proven only with XFG (OR=3.592, p<0.001). Neither of the two LOXL1 SNPs was significantly associated with POAG. CONCLUSIONS: We confirmed the association between LOXL1 and XFS/XFG, but the APOE and MTHFR polymorphisms are not significant risk factors for the development of XFS/XFG in our population of patients from Epirus (Greece)