Epigenetics in diagnosis, prognostic assessment and treatment of cancer:An update

Cancer cells contain multiple genetic and epigenetic changes. The relative specificity of many epigenetic changes for neoplastic cells has allowed the identification of diagnostic, prognostic and predictive biomarkers for a number of solid tumors and hematological malignancies. Moreover, epigenetically-acting drugs are already in routine use for cancer and numerous additional agents are in clinical trials. Here, we review recent progress in the development and application of epigenetic strategies for the diagnosis, risk stratification and treatment of cancer

The Role of Non-Coding RNAs in Myelodysplastic Neoplasms

Myelodysplastic syndromes or neoplasms (MDS) are a heterogeneous group of myeloid clonal disorders characterized by peripheral blood cytopenias, blood and marrow cell dysplasia, and increased risk of evolution to acute myeloid leukemia (AML). Non-coding RNAs, especially microRNAs and long non-coding RNAs, serve as regulators of normal and malignant hematopoiesis and have been implicated in carcinogenesis. This review presents a comprehensive summary of the biology and role of non-coding RNAs, including the less studied circRNA, siRNA, piRNA, and snoRNA as potential prognostic and/or predictive biomarkers or therapeutic targets in MDS

The human platelet: strong transcriptome correlations among individuals associate weakly with the platelet proteome.

BACKGROUND: For the anucleate platelet it has been unclear how well platelet transcriptomes correlate among different donors or across different RNA profiling platforms, and what the transcriptomes\u27 relationship is with the platelet proteome. We profiled the platelet transcriptome of 10 healthy young males (5 white and 5 black) with no notable clinical history using RNA sequencing and by Affymetrix microarray. RESULTS: We found that the abundance of platelet mRNA transcripts was highly correlated across the 10 individuals, independently of race and of the employed technology. Our RNA-seq data showed that these high inter-individual correlations extend beyond mRNAs to several categories of non-coding RNAs. Pseudogenes represented a notable exception by exhibiting a difference in expression by race. Comparison of our mRNA signatures to a publicly available quantitative platelet proteome showed that most (87.5%) identified platelet proteins had a detectable corresponding mRNA. However, a high number of mRNAs that were present in the transcriptomes of all 10 individuals had no representation in the proteome. Spearman correlations of the relative abundances for those genes represented by both an mRNA and a protein showed a weak (~0.3) connection. Further analysis of the overlapping and non-overlapping platelet mRNAs and proteins identified gene groups corresponding to distinct cellular processes. CONCLUSIONS: The results of our analyses provide novel insights for platelet biology, show only a weak connection between the platelet transcriptome and proteome, and indicate that it is feasible to assemble a platelet mRNA-ome that can serve as a reference for future platelet transcriptomic studies of human health and disease. REVIEWED BY: This article was reviewed by Dr Mikhail Dozmorov (nominated by Dr Yuri Gusev), Dr Neil Smalheiser and Dr Eugene Koonin

Study of the expression and clinical significance of cyclins and the methylation status of their inhibitors in haemotological malignancies

Aim of this study was to study the expression of type D cyclins and the methylation status of genes that are involved in cell cycle regulation pathways (CDKN2B, CDKN2A,CDKN1C, TP73, Snk/plk2, VHL) in patients with monoclonal gammopathies. Patients and methods: We studied 45 patients with multiple myeloma (MM), 4 patients with Waldenstrom's macroglobulinemia (WM), and 3 patients with monoclonal gammopathy of undetermined significance (MGUS). Quantitative RT-PCR was employed for the cyclin expression. Methylation status of each gene was analysed by methylation-specific PCR (MSP). Logistic regression analysis where gene methylation status at diagnosis was used as a single predictor variable to measure associations with the development of anemia, advanced stage disease, extramedullary disease and bone disease (all as the dependent variables). Survival curves were generated using the method of Kaplan-Meier and compared with the log-rank test. Results: Increased expression of D type cyclins was noted in MM patients. Cyclin D1 levels were significantly higher to cyclin D2 levels (p=0.01) and cyclin D3 (p=0.004). Interesting associations were noted between cyclin expression levels and relevant clinical parameters but no significant prognostic value was found. Methylation of the p15 (CDKN4B) and p16 (CDKN4A) was found in 28% and 31 % of MM patients respectively. Patients methylated for p16 were more likely to have advanced stage disease and anemia at diagnosis and had an increased risk of death, but p values did not reach significance. Methylation of p16 was not found to be a predictor of bone or extramedullary disease. Patients methylated for the p15 promoter were more likely to have anemia at diagnosis (p>0.05). No association was found between p15 methylation status and bone or extramedullary disease or overall survival. No patient was found to be methylated for CDKN1C and TP73. Methylation of the VHL promoter was found in 41 % of MM patients. Patients methylated for VHL showed an increased risk of death (HR=1.3, p=0.6), anemia (OR=2, p=0.2), extramedullary disease (OR=2.3, p=0.22) and significantly increased risk of developing development of lytic bone disease (OR =6.5, p=0.029). Snk/plk2 methylation was noted in 60% and 75% of MM and WM patients respectively. No significant association was found between snk/plk2 methylation and clinical parameters. In summary, cyclins are overexpressed in MM, but they do not hold a significant prognostic value. Genes involved in cell cycle regulation are found to be methylated in MM and WM. Several interesting trends were noted between the genes methylation status and relevant clinical parameters. These findings warrant further evaluation in a larger sample of patients in order to enhance our statistical power and better define the prognostic value of each gene's methylation status in these diseases.Σκοπός της παρούσας διατριβής ήταν να μελετηθούν γονίδια που συμμετέχουν στη ρύθμιση του κυτταρικού κύκλου, αλλά και οι επιγενετικές αλλαγές, μέσω μεθυλίωσης που αυτά μπορεί να έχουν υποστεί. Συγκεκριμένα μελετήθηκε η έκφραση και η κλινική σημασία των κυκλινών DI, D2 και D3, ενώ επιπλέον μελετήθηκε και η μεθυλίωση γονιδίων που συμμετέχουν στη ρύθμιση του κυτταρικού κύκλου (CDKN4B, CDKN4A, CDKN1C, ΤΡ73, Snk/plk2, VHL) σε ασθενείς με μονοκλωνικές γαμμαπάθειες. Ασθενείς και Μέθοδοι. Μελετήθηκαν 45 ασθενείς με πολλαπλό μυέλωμα (ΠΜ), 4 ασθενείς με Μακροσφαιριναιμία Waldenström (MW) και 3 άνδρες ασθενείς με μονοκλωνική γαμμαπάθεια αδιευκρίνιστης σημασίας (ΜΓΑΣ). Η μελέτη της έκφρασης των κυκλινών τύπου D έγινε με τη μέθοδο RT-PCR. Η μελέτη της μεθυλίωσης των υποκινητών των γονιδίων έγινε με MSP (methylation specific PCR). Χρησιμοποιήθηκε η ανάλυση απλής λογιστικής παλινδρόμησης για να εκτιμηθεί η συσχέτιση με κλινικές παραμέτρους. Οι καμπύλες εκτίμησης επιβίωσης έγιναν με τη χρήση της μεθόδου Kaplan Meier και η σύγκρισή τους με τη μέθοδο log-rank. Αποτελέσματα. Στους ασθενείς με πολλαπλό μυέλωμα παρατηρήθηκε αυξημένη έκφραση των κυκλινών τύπου D. Οι τιμές της κυκλίνης D1 ήταν στατιστικώς σημαντικά υψηλότερες σε σχέση με τις τιμές της κυκλίνης D2 (p=0.01) και τις τιμές της D3 (p=0.004). Στατιστική ανάλυση της σχέσης των κυκλινών με κλινικές παραμέτρους ανέδειξε ενδιαφέρουσες τάσεις, χωρίς όμως να βρεθεί ιδιαίτερη προγνωστική αξία. Μεθυλίωση του CDKN2B και του CDKN2A παρατηρήθηκε σε ασθενείς με ΠΜ, σε ποσοστό 28% και 31 % αντίστοιχα. Ασθενείς με μεθυλιωμένο το CDKN2A είχαν την τάση να έχουν προχωρημένο στάδιο νόσου και αναιμία κατά τη διάγνωση και ο κίνδυνος να καταλήξουν ήταν 1,9 φορές πιο μεγάλος, διαφορά όμως στατιστικώς μη σημαντική. Ασθενείς με μεθυλιωμένο το CDKN2B είχαν την τάση να έχουν αναιμία κατά τη διάγνωση, αλλά δε βρέθηκε συσχέτιση με την παρουσία εξωμυελικής ή οστικής νόσου ή τη συνολική επιβίωση. Σε κανένα από τους ασθενείς δε βρέθηκε μεθυλίωση του CDKN1C και του ΤΡ73. Το ποσοστό των ασθενών με ΠΜ που βρέθηκε να έχει μεθυλίωση για το VHL ήταν 41%. Οι ασθενείς με μεθυλιωμένο υποκινητή του VHL είχαν μεγαλύτερο κίνδυνο να καταλήξουν (HR=1.3, p=0.6), να έχουν αναιμία (OR=2.0, p=0.2), να έχουν εξωμυελική νόσο (OR=2.3, p=0.228) και στατιστικώς σημαντικά αυξημένο κίνδυνο (κατά 6,5 φορές) εμφάνισης οστικής νόσου (p=0.018). Μεθυλίωση του snk/plk2 παρατηρήθηκε στο 60% και 75% ασθενών με ΠΜ και MW αντίστοιχα. Η κατάσταση μεθυλίωσης του snk/plk2 δεν ήταν προγνωστικός δείκτης της συνολικής επιβίωσης, ή άλλων σχετικών κλινικών παραμέτρων. Συμπεράσματα. Οι κυκλίνες παρουσιάζουν υπερέκφραση στο πολλαπλό μυέλωμα, αλλά δεν παρουσιάζουν ιδιαίτερη προγνωστική άξια. Ασθενείς με ΠΜ και MW, παρουσιάζουν μεθυλίωση γονιδίων που σχετίζονται με τη ρύθμιση του κυτταρικού κύκλου. Η κατάσταση μεθυλίωσης του VHL μπορεί να χρησιμοποιηθεί ως προγνωστικός δείκτης ανάπτυξης οστικής νόσου σε ασθενείς με ΠΜ. Ενδιαφέρουσες τάσεις συσχέτισης της κατάστασης μεθυλίωσης και κλινικοεργαστηριακών παραμέτρων χρήζουν περαιτέρω διερεύνησης για να διευκρινιστεί και να καθοριστεί η προγνωστική τους αξία

Interpreting results from oncology clinical trials: a comparison of denosumab to zoledronic acid for the prevention of skeletal-related events in cancer patients

BACKGROUND: Critically reviewing the design, endpoints, and results of clinical trials can be challenging to health care professionals. This paper will review the basic methods of presenting clinical outcomes in randomized trials and will focus on the number needed to treat (NNT) concept. NNT will then be applied to the case of bone-targeted therapies denosumab and zoledronic acid, which are used for the prevention of skeletal-related events (SREs) in a variety of disease sites. METHODS: A Medline search was performed to identify randomized trials comparing denosumab to zoledronic acid for the prevention of SREs in patients with advanced breast, prostate, and other cancer sites. The data were extracted, and point estimates for the primary and secondary trial endpoints were converted into the NNT parameter. RESULTS: NNT represents the number of patients that need to be treated with a new intervention in order to avoid one additional patient developing the event and is a powerful approach that can be used to make sense of numerical results from clinical trials. In patients with advanced breast, prostate, and other cancer sites, 18, 22, and 21 patients, respectively, would need to be treated with denosumab for at least 24 months to avoid one patient developing an SRE. CONCLUSIONS: The NNT approach is a simple and effective method to express the findings of randomized trials in a clinically meaningful way. In this analysis, the incremental benefits of denosumab would be realized when a minimum of 18 to 22 patients are treated for a prolonged duration. Clinicians would have to weigh the costs and benefits between denosumab and zoledronic acid when bone-targeted therapy is indicated

Luspatercept: A New Tool for the Treatment of Anemia Related to β-Thalassemia, Myelodysplastic Syndromes and Primary Myelofibrosis

Anemia is a common feature of both benign and malignant hematologic diseases. Beta-thalassemia (β-thalassemia) syndromes are a group of hereditary disorders characterized by ineffective erythropoiesis, due to a genetic deficiency in the synthesis of the beta chains of hemoglobin, often accompanied by severe anemia and the need for red blood cell (RBC) transfusions. Myelodysplastic syndromes (MDS) are characterized by cytopenia(s) and ineffective hematopoiesis, despite a hypercellular bone marrow. Primary myelofibrosis (PMF) is a clonal myeloproliferative neoplasm characterized by reactive fibrosis of the bone marrow, accompanied by extramedullary hematopoiesis. Luspatercept, previously known as ACE-536, is a fusion protein that combines a modified activin receptor IIB (ActRIIB), a member of the transforming growth factor-β (TGF-β) superfamily, with the Fc domain of human immunoglobulin G (IgG1). It has shown efficacy in the treatment of anemia due to beta β-thalassemia, MDS and PMF and recently gained approval by the Federal Drug Agency (FDA) and the European Medicines Agency (EMA) for transfusion-dependent (TD) patients with β-thalassemia and very low to intermediate-risk patients with MDS with ringed sideroblasts who have failed to respond to, or are ineligible for, an erythropoiesis-stimulating agent. In this review, we describe the key pathways involved in normal hematopoiesis and the possible mechanism of action of luspatercept, present its development and data from the most recent clinical trials in β-thalassemia, MDS and PMF, and discuss its potential use in the treatment of these hematological disorders