Novel genetic risk variants for pediatric celiac disease

Background: Celiac disease is a complex chronic immune-mediated disorder of the small intestine. Today, the pathobiology of the disease is unclear, perplexing differential diagnosis, patient stratification, and decision-making in the clinic. Methods: Herein, we adopted a next-generation sequencing approach in a celiac disease trio of Greek descent to identify all genomic variants with the potential of celiac disease predisposition. Results: Analysis revealed six genomic variants of prime interest: SLC9A4 c.1919G gt A, KIAA1109 c.2933T gt C and c. 4268_4269delCCinsTA, HoxB6 c.668C gt A, HoxD12 c.418G gt A, and NCK2 c.745_746delAAinsG, from which NCK2 c.745_746delAAinsG is novel. Data validation in pediatric celiac disease patients of Greek (n=109) and Serbian (n=73) descent and their healthy counterparts (n=111 and n=32, respectively) indicated that HoxD12 c.418G gt A is more prevalent in celiac disease patients in the Serbian population (P lt 0.01), while NCK2 c.745_746delAAinsG is less prevalent in celiac disease patients rather than healthy individuals of Greek descent (P = 0. 03). SLC9A4 c.1919G gt A and KIAA1109 c.2933T gt C and c.4268_4269delCCinsTA were more abundant in patients; nevertheless, they failed to show statistical significance. Conclusions: The next-generation sequencing-based family genomics approach described herein may serve as a paradigm towards the identification of novel functional variants with the aim of understanding complex disease pathobiology

Correlation of genomic biomarkers in KLF family genes with fetal hemoglobin levels in humans: expansion on individualized hydroxyurea treatment of patients suffering from β-type hemoglobinopathies

Hemoglobinopathies, including sickle-cell disease (SCD) and beta-thalassemia are among the most common monogenic disorders worldwide. They are mainly characterized by either defective or downrated to absent synthesis of one of the two polypeptide chains of hemoglobin. To date, the therapeutic options for treatment are limited. One of the most promising therapeutic approaches is the induction of γ globin genes, in order to increase the fetal hemoglobin levels and, as a result, to improve the patients`clinical picture. Thus, a large number of studies currently focus on transcription factors involved in the regulation of fetal hemoglobin.The only drug found to transiently reactivate the γ globin levels in patients suffering from SCD, and which is currently approved by the Food and Drug Administration (FDA) is hydroxyurea (HU). Several studies regarding HU administration in β-type hemoglobinopathies resulted in highly variable responses among patients to HU.Kruppel like factors (KLFs) constitute a family of transcription factors with a wide range of functions, including the regulation of the expression of globin genes during the different human developmental stages.At the current study, four tagSNPs (tagging single nucleotide polymorphisms), namely the rs2242189, rs2236599, rs11142398 and rs980112, located in four different Klf genes (Klf3, Klf4, Klf9 and Klf10 respectively) were studied, in order to examine (i) whether they were associated with increased HbF levels, thus affecting the β-thalassemia patients` condition, and (ii) their possible association with HU response in double heterozygous (SCD and beta-thalassaemia) patients. For this purpose, blood samples from (a) healthy non-thalassemic individuals; (b) transfusion-dependent beta-thalassemic patients; (c) non-transfusion-dependent beta thalassemic patients and (d) double heterozygous (SCD/b-thal) patients were analyzed by genotyping the abovementioned SNPs. The double heterozygous patients, to whom HU was administered, were divided into responders and non-responders to HU treatment, using two different criteria: (i) the increase of HbF levels above 20% and (ii) the three-fold increase of HbF levels.Target sequences were amplified by PCR and genotyped by either RFLP (restriction fragment length polymorphism) or Sanger chromosequencing; statistical analysis on the genotypes` and alleles` frequencies followed.The results of our study showed that under the >20% level increase criterion the rs2236599, located in Klf4, seems to be related (p=0,0396) with the response of double heterozygous patients to HU and that rs980112, located in Klf10, seems to be associated (p=0,0431) with the increased fetal hemoglobin levels on non-transfusion-dependent thalassemia patients.Οι αιμοσφαιρινοπάθειες, συμπεριλαμβανομένης της δρεπανοκυτταρικής αναιμίας και της β-θαλασσαιμίας, συγκαταλέγονται ανάμεσα στις πλέον κοινές μονογονιδιακές διαταραχές παγκοσμίως. Γνώρισμά τους είναι οι ανωμαλίες είτε στη δομή είτε στην ποσότητα μιας εκ των δύο σφαιρινικών υπομονάδων α και β. Ως και σήμερα, οι θεραπευτικές προσεγγίσεις για την αντιμετώπισή τους είναι περιορισμένες. Ένας τρόπος θεραπείας που θεωρείται πολλά υποσχόμενος είναι η επαγωγή της γ-σφαιρίνης, με απώτερο σκοπό την αύξηση των επιπέδων της εμβρυικής αιμοσφαιρίνης HbF, προς βελτίωση της κλινικής εικόνας των ασθενών.Η μοναδική φαρμακευτική ουσία που έχει λάβει την έγκριση του Οργανισμού Τροφίμων και Φαρμάκων των Ηνωμένων Πολιτειών Αμερικής (FDA) για την επαγωγή της HbF σε δρεπανοκυτταρικούς ασθενείς είναι η υδροξυουρία (HU). Υπάρχει πληθώρα μελετών που αφορούν τη χορήγηση της HU σε πάσχοντες από β-θαλασσαιμία και που έχουν καταδείξει μεγάλη ετερογένεια στην ανταπόκριση των ασθενών σε αυτή. Έτσι, ένας μεγάλος αριθμός αυτών των μελετών επικεντρώνεται στους μεταγραφικούς παράγοντες που συμμετέχουν στη ρύθμιση της παραγωγής της εμβρυικής αιμοσφαιρίνης.Μια τέτοια οικογένεια μεταγραφικών παραγόντων είναι και αυτοί της οικογένειας τύπου Kruppel, οι οποίοι μεσολαβούν στην εναλλαγή της έκφρασης των γονιδίων των δύο σφαιρινικών συμπλεγμάτων (α και β) στη μεταστροφή των αιμοσφαιρινών κατά την ανάπτυξη. Στην παρούσα μελέτη εξετάστηκαν 4 μονονουκλεοτιδικοί πολυμορφισμοί επισήμανσης που εδράζονται σε 4 γονίδια Klf (συγκεκριμένα, οι πολυμορφισμοί rs2242189, rs2236599, rs11142398 και rs980112 των γονιδίων Klf3, Klf4, Klf9, Klf10 αντιστοίχως). Διερευνήθηκε τόσο η πιθανή τους συσχέτιση με τα αυξημένα επίπεδα της εμβρυικής αιμοσφαιρίνης, άρα και με την ηπιότερη κλινική εικόνα των β-θαλασσαιμικών ασθενών, όσο και η αντίστοιχη πιθανή συσχέτισή τους με την ανταπόκριση των διπλών ετεροζυγωτών σε β-θαλασσαιμία και δρεπανοκυτταρική αναιμία ασθενών στην θεραπεία με υδροξυουρία. Χρησιμοποιήθηκαν δείγματα (i) ατόμων υγιών, (ii) πασχόντων από εξαρτώμενη μεταγγίσεων β-θαλασσαιμία, (iii) πασχόντων από μη εξαρτώμενη μεταγγίσεων β-θαλασσαιμία και (iv) διπλά ετερόζυγων σε β-θαλασσαιμία και δρεπανοκυτταρική αναιμία, που λάμβαναν ως θεραπευτική αγωγή την υδροξυουρία. Η τελευταία κατηγορία πασχόντων διακρίθηκε περαιτέρω σε ανταποκρινόμενους στη θεραπεία με HU και σε μη ανταποκρινόμενους στη συγκεκριμένη θεραπεία με τη χρήση δύο κριτηρίων: του κριτηρίου αύξησης των επιπέδων της HbF σε ποσοστό μεγαλύτερο του 20% και του κριτηρίου τριπλασιασμού τους. Η ενίσχυση των αλληλουχιών πραγματοποιήθηκε με αλυσιδωτή αντίδραση πολυμεράσης και η γονοτύπηση είτε με RFLP ή με αλληλούχηση κατά Sanger. Ακολούθησε η στατιστική επεξεργασία των συχνοτήτων, τόσο στα αλληλόμορφα όσο και στους γονοτύπους των μελετούμενων ενδεικτικών πολυμορφισμών.Τα αποτελέσματα της στατιστικής ανάλυσης κατέδειξαν (Ι) πως ο πολυμορφισμός rs2236599 του Klf4 σχετίζεται πιθανώς (p=0,0396) με την ανταπόκριση των διπλά ετερόζυγων ασθενών στην υδροξυουρία (βάσει του κριτηρίου αύξησης των επιπέδων της HbF σε ποσοστό μεγαλύτερο του 20%) και (ΙΙ) πως ο πολυμορφισμός rs980112 του Klf10 είναι πιθανό να σχετίζεται σημαντικά (p=0,0431) με αυξημένα επίπεδα εμβρυικής αιμοσφαιρίνης HbF στους ασθενείς με μη εξαρτώμενη μεταγγίσεων β-θαλασσαιμία και, συνεπώς, με την ηπιότερη κλινική τους εικόνα

Novel genetic risk variants for pediatric celiac disease

Background: Celiac disease is a complex chronic immune-mediated disorder of the small intestine. Today, the pathobiology of the disease is unclear, perplexing differential diagnosis, patient stratification, and decision-making in the clinic.Methods: Herein, we adopted a next-generation sequencing approach in a celiac disease trio of Greek descent to identify all genomic variants with the potential of celiac disease predisposition.Results: Analysis revealed six genomic variants of prime interest: SLC9A4 c.1919G>A, KIAA1109 c.2933T>C and c.4268_4269delCCinsTA, HoxB6 c.668C>A, HoxD12 c.418G>A, and NCK2 c.745_746delAAinsG, from which NCK2 c.745_746delAAinsG is novel. Data validation in pediatric celiac disease patients of Greek (n = 109) and Serbian (n = 73) descent and their healthy counterparts (n = 111 and n = 32, respectively) indicated that HoxD12 c.418G>A is more prevalent in celiac disease patients in the Serbian population (P A and KIAA1109 c.2933T>C and c.4268_4269delCCinsTA were more abundant in patients; nevertheless, they failed to show statistical significance.Conclusions: The next-generation sequencing-based family genomics approach described herein may serve as a paradigm towards the identification of novel functional variants with the aim of understanding complex disease pathobiology.peer-reviewe

Clinical implementation of preemptive pharmacogenomics in psychiatryResearch in context

Summary: Background: Pharmacogenomics (PGx) holds promise to revolutionize modern healthcare. Although there are several prospective clinical studies in oncology and cardiology, demonstrating a beneficial effect of PGx-guided treatment in reducing adverse drug reactions, there are very few such studies in psychiatry, none of which spans across all main psychiatric indications, namely schizophrenia, major depressive disorder and bipolar disorder. In this study we aim to investigate the clinical effectiveness of PGx-guided treatment (occurrence of adverse drug reactions, hospitalisations and re-admissions, polypharmacy) and perform a cost analysis of the intervention. Methods: We report our findings from a multicenter, large-scale, prospective study of pre-emptive genome-guided treatment named as PREemptive Pharmacogenomic testing for preventing Adverse drug REactions (PREPARE) in a large cohort of psychiatric patients (n = 1076) suffering from schizophrenia, major depressive disorder and bipolar disorder. Findings: We show that patients with an actionable phenotype belonging to the PGx-guided arm (n = 25) present with 34.1% less adverse drug reactions compared to patients belonging to the control arm (n = 36), 41.2% less hospitalisations (n = 110 in the PGx-guided arm versus n = 187 in the control arm) and 40.5% less re-admissions (n = 19 in the PGx-guided arm versus n = 32 in the control arm), less duration of initial hospitalisations (n = 3305 total days of hospitalisation in the PGx-guided arm from 110 patients, versus n = 6517 in the control arm from 187 patients) and duration of hospitalisation upon readmission (n = 579 total days of hospitalisation upon readmission in the PGx-guided arm, derived from 19 patients, versus n = 928 in the control arm, from 32 patients respectively). It was also shown that in the vast majority of the cases, there was less drug dose administrated per drug in the PGx-guided arm compared to the control arm and less polypharmacy (n = 124 patients prescribed with at least 4 psychiatric drugs in the PGx-guided arm versus n = 143 in the control arm) and smaller average number of co-administered psychiatric drugs (2.19 in the PGx-guided arm versus 2.48 in the control arm. Furthermore, less deaths were reported in the PGx-guided arm (n = 1) compared with the control arm (n = 9). Most importantly, we observed a 48.5% reduction of treatment costs in the PGx-guided arm with a reciprocal slight increase of the quality of life of patients suffering from major depressive disorder (0.935 versus 0.925 QALYs in the PGx-guided and control arm, respectively). Interpretation: While only a small proportion (∼25%) of the entire study sample had an actionable genotype, PGx-guided treatment can have a beneficial effect in psychiatric patients with a reciprocal reduction of treatment costs. Although some of these findings did not remain significant when all patients were considered, our data indicate that genome-guided psychiatric treatment may be successfully integrated in mainstream healthcare. Funding: European Union Horizon 2020

Additional file 1: of Novel genetic risk variants for pediatric celiac disease

A seven-member Greek family has been recruited (informed consents have been obtained), and a trio analysis (III-1, III-2, IV-3) has been performed using the celiac disease model. (PNG 136 kb

Additional file 2: of Novel genetic risk variants for pediatric celiac disease

Regulome DB questioned a possible role of the variants of interest in terms of transcription factor binding sites, chromatin states, eQTLs, differentially methylated regions, validated functional SNPs and DNase sensitivity. All variants had minimum or no impact. (XLSX 3.62 mb

A 12-gene pharmacogenetic panel to prevent adverse drug reactions: an open-label, multicentre, controlled, cluster-randomised crossover implementation study

© 2023Background: The benefit of pharmacogenetic testing before starting drug therapy has been well documented for several single gene–drug combinations. However, the clinical utility of a pre-emptive genotyping strategy using a pharmacogenetic panel has not been rigorously assessed. Methods: We conducted an open-label, multicentre, controlled, cluster-randomised, crossover implementation study of a 12-gene pharmacogenetic panel in 18 hospitals, nine community health centres, and 28 community pharmacies in seven European countries (Austria, Greece, Italy, the Netherlands, Slovenia, Spain, and the UK). Patients aged 18 years or older receiving a first prescription for a drug clinically recommended in the guidelines of the Dutch Pharmacogenetics Working Group (ie, the index drug) as part of routine care were eligible for inclusion. Exclusion criteria included previous genetic testing for a gene relevant to the index drug, a planned duration of treatment of less than 7 consecutive days, and severe renal or liver insufficiency. All patients gave written informed consent before taking part in the study. Participants were genotyped for 50 germline variants in 12 genes, and those with an actionable variant (ie, a drug–gene interaction test result for which the Dutch Pharmacogenetics Working Group [DPWG] recommended a change to standard-of-care drug treatment) were treated according to DPWG recommendations. Patients in the control group received standard treatment. To prepare clinicians for pre-emptive pharmacogenetic testing, local teams were educated during a site-initiation visit and online educational material was made available. The primary outcome was the occurrence of clinically relevant adverse drug reactions within the 12-week follow-up period. Analyses were irrespective of patient adherence to the DPWG guidelines. The primary analysis was done using a gatekeeping analysis, in which outcomes in people with an actionable drug–gene interaction in the study group versus the control group were compared, and only if the difference was statistically significant was an analysis done that included all of the patients in the study. Outcomes were compared between the study and control groups, both for patients with an actionable drug–gene interaction test result (ie, a result for which the DPWG recommended a change to standard-of-care drug treatment) and for all patients who received at least one dose of index drug. The safety analysis included all participants who received at least one dose of a study drug. This study is registered with ClinicalTrials.gov, NCT03093818 and is closed to new participants. Findings: Between March 7, 2017, and June 30, 2020, 41 696 patients were assessed for eligibility and 6944 (51·4 % female, 48·6% male; 97·7% self-reported European, Mediterranean, or Middle Eastern ethnicity) were enrolled and assigned to receive genotype-guided drug treatment (n=3342) or standard care (n=3602). 99 patients (52 [1·6%] of the study group and 47 [1·3%] of the control group) withdrew consent after group assignment. 652 participants (367 [11·0%] in the study group and 285 [7·9%] in the control group) were lost to follow-up. In patients with an actionable test result for the index drug (n=1558), a clinically relevant adverse drug reaction occurred in 152 (21·0%) of 725 patients in the study group and 231 (27·7%) of 833 patients in the control group (odds ratio [OR] 0·70 [95% CI 0·54–0·91]; p=0·0075), whereas for all patients, the incidence was 628 (21·5%) of 2923 patients in the study group and 934 (28·6%) of 3270 patients in the control group (OR 0·70 [95% CI 0·61–0·79]; p <0·0001). Interpretation: Genotype-guided treatment using a 12-gene pharmacogenetic panel significantly reduced the incidence of clinically relevant adverse drug reactions and was feasible across diverse European health-care system organisations and settings. Large-scale implementation could help to make drug therapy increasingly safe. Funding: European Union Horizon 2020