CLINICAL AND CYTOGENETIC FEATURES OF LEUKEMIAS IN CHILDREN TREATED IN THE UNIVERSITY HOSPITAL OF SPLIT FROM 2000 TO 2017

Objectives: Pediatric leukemias are generally characterized by recurrent genetic aberrations, which are thought to be specifically associated with diagnosis and prognosis. The aim of the study was to investigate the frequency and types of acquired chromosomal aberrations and correlation with other biological characteristics and prognostic risk factors. Materials and methods: We retrospectively reviewed clinical features and results of cytogenetics and molecular analysis for patients younger than 18 years with newly diagnosed pediatric leukemia from January 2000 to December 2017. Results: In an 18-year period, 98 children with pediatric leukemia were hospitalized, 47 girls (48 %) and 51 boys (52 %). We had 76 patients diagnosed with ALL (77%), 20 with AML (21%), and 2 with CML (2%). Fever, pallor, lymphadenopathy, and hepatomegaly were the four most common presenting symptoms of leukemia in children (more than 50%). Among all patients, 29% had normal karyotype while 71% had acquired numerical and/or structural chromosomal aberrations. The most frequent chromosomal aberrations in pediatric ALL were t(12;21) ETV6/RUNX1 fusion gene (27%) and hyperdiploidy (15%), both associated with prognostic favorable outcomes and B cell lineage immunophenotype. In AML subgroup, the most frequent chromosomal aberration was translocation t(8;21) with RUNX1-RUNX1T1 fusion gene (21%), slightly higher than reported in the 2008 WHO Classification. On the other hand, the frequency of 11q23 MLL-rearrangements, t(15;17) with PML-RARA fusion gene, inv(16) or del(16q), deletion -7/del(7q) was in accordance to the literature. Two patients were diagnosed with CML, Ph-positive. Conclusion: In this study, the frequency of various acquired chromosomal aberrations as well as their correlation with clinical and biological risk factors in a group of children with newly diagnosed leukemia are similar to previously published studies at pediatric population in Europe and US.Uvod: Pedijatrijske leukemije općenito su karakterizirane ponavljajućim genetičkim aberacijama, a za koje se smatra da su specifično povezane s dijagnozom i prognozom. Cilj istraživanja bio je ispitati učestalost i vrste stečenih kromosomskih aberacija i usporediti ih s drugim biološkim karakteristikama i prognostičkim čimbenicima rizika. Materijali i metode: Retrospektivnim istraživanjem prikazali smo kliničku sliku i rezultate citogenetičke i molekularne analize kod pacijenata mlađih od 18 godina sa novodijagnosticiranom pedijatrijskom leukemijom u periodu od siječnja 2000. do prosinca 2017. godine. Rezultati: U osamnestogodišnjem razdoblju leukemija je dijagnosticiranau 98 djece, 47 djevojčica (48%) i 51 dječaka (52%). Od toga 76 pacijenata imalo je dijagnozu ALL (77%), 20 AML (21%), i 2 CML (2%).Više od 50% djece imalo je četiri najčešća simptoma leukemije:vrućicu, bljedilo, limfadenopatiju i hepatomegaliju.Od svih pacijenata uredan kariotip imalo je 29% pacijenata dok je 71% imalo stečene numeričke i/ili strukturne kromosomske aberacije.Najučestalije aberacije u pedijatrijskoj ALL bile su t(12;21) s fuzijom ETV6/RUNX1 gena (27%) i hiperploidija (15%), a obje su povezane sa prognostički povoljnim ishodom i B staničnim imunofenotipom. U grupi djece sa AML najučestalija kromosomska aberacija bila je t(8;21)s fuzijom gena RUNX1/RUNXT1(21%), nešto viša nego što je objavljeno u klasifikaciji SZO 2008. S druge strane učestalost 11q23 MLL- preuređenja, t(15;17) s fuzijom PML-RARA gena, inv (16) ili del (16q), -7/del(7q) bile su u skladu s podacima iz literature. Philadelphiapozitivnu CML leukemiju imalo je dvoje djece. Zaključak: Učestalost i raznolikost stečenih kromosomskih aberacija upedijatrijskim leukemijama iz našestudijekao i njihova povezanost s kliničkim i biološkim prognostičkim čimbenicima slična je podacima iz literature za pedijatrijsku populaciju u Europi i SAD-u

CLINICAL AND CYTOGENETIC FEATURES OF LEUKEMIAS IN CHILDREN TREATED IN THE UNIVERSITY HOSPITAL OF SPLIT FROM 2000 TO 2017

Objectives: Pediatric leukemias are generally characterized by recurrent genetic aberrations, which are thought to be specifically associated with diagnosis and prognosis. The aim of the study was to investigate the frequency and types of acquired chromosomal aberrations and correlation with other biological characteristics and prognostic risk factors. Materials and methods: We retrospectively reviewed clinical features and results of cytogenetics and molecular analysis for patients younger than 18 years with newly diagnosed pediatric leukemia from January 2000 to December 2017. Results: In an 18-year period, 98 children with pediatric leukemia were hospitalized, 47 girls (48 %) and 51 boys (52 %). We had 76 patients diagnosed with ALL (77%), 20 with AML (21%), and 2 with CML (2%). Fever, pallor, lymphadenopathy, and hepatomegaly were the four most common presenting symptoms of leukemia in children (more than 50%). Among all patients, 29% had normal karyotype while 71% had acquired numerical and/or structural chromosomal aberrations. The most frequent chromosomal aberrations in pediatric ALL were t(12;21) ETV6/RUNX1 fusion gene (27%) and hyperdiploidy (15%), both associated with prognostic favorable outcomes and B cell lineage immunophenotype. In AML subgroup, the most frequent chromosomal aberration was translocation t(8;21) with RUNX1-RUNX1T1 fusion gene (21%), slightly higher than reported in the 2008 WHO Classification. On the other hand, the frequency of 11q23 MLL-rearrangements, t(15;17) with PML-RARA fusion gene, inv(16) or del(16q), deletion -7/del(7q) was in accordance to the literature. Two patients were diagnosed with CML, Ph-positive. Conclusion: In this study, the frequency of various acquired chromosomal aberrations as well as their correlation with clinical and biological risk factors in a group of children with newly diagnosed leukemia are similar to previously published studies at pediatric population in Europe and US.Uvod: Pedijatrijske leukemije općenito su karakterizirane ponavljajućim genetičkim aberacijama, a za koje se smatra da su specifično povezane s dijagnozom i prognozom. Cilj istraživanja bio je ispitati učestalost i vrste stečenih kromosomskih aberacija i usporediti ih s drugim biološkim karakteristikama i prognostičkim čimbenicima rizika. Materijali i metode: Retrospektivnim istraživanjem prikazali smo kliničku sliku i rezultate citogenetičke i molekularne analize kod pacijenata mlađih od 18 godina sa novodijagnosticiranom pedijatrijskom leukemijom u periodu od siječnja 2000. do prosinca 2017. godine. Rezultati: U osamnestogodišnjem razdoblju leukemija je dijagnosticiranau 98 djece, 47 djevojčica (48%) i 51 dječaka (52%). Od toga 76 pacijenata imalo je dijagnozu ALL (77%), 20 AML (21%), i 2 CML (2%).Više od 50% djece imalo je četiri najčešća simptoma leukemije:vrućicu, bljedilo, limfadenopatiju i hepatomegaliju.Od svih pacijenata uredan kariotip imalo je 29% pacijenata dok je 71% imalo stečene numeričke i/ili strukturne kromosomske aberacije.Najučestalije aberacije u pedijatrijskoj ALL bile su t(12;21) s fuzijom ETV6/RUNX1 gena (27%) i hiperploidija (15%), a obje su povezane sa prognostički povoljnim ishodom i B staničnim imunofenotipom. U grupi djece sa AML najučestalija kromosomska aberacija bila je t(8;21)s fuzijom gena RUNX1/RUNXT1(21%), nešto viša nego što je objavljeno u klasifikaciji SZO 2008. S druge strane učestalost 11q23 MLL- preuređenja, t(15;17) s fuzijom PML-RARA gena, inv (16) ili del (16q), -7/del(7q) bile su u skladu s podacima iz literature. Philadelphiapozitivnu CML leukemiju imalo je dvoje djece. Zaključak: Učestalost i raznolikost stečenih kromosomskih aberacija upedijatrijskim leukemijama iz našestudijekao i njihova povezanost s kliničkim i biološkim prognostičkim čimbenicima slična je podacima iz literature za pedijatrijsku populaciju u Europi i SAD-u

Beyond Large Complex Structure: Quantized Periods and Boundary Data for One-Modulus Singularities

We study periods in an integral basis near all possible singularities in one-dimensional complex structure moduli spaces of Calabi-Yau threefolds. Near large complex structure points these asymptotic periods are well understood in terms of the topological data of the mirror Calabi-Yau manifold. The aim of this work is to characterize the period data near other boundaries in moduli space such as conifold and K-points. Using results from Hodge theory, we provide the general form of these periods in a quantized three-cycle basis. Based on these periods we compute the prepotential and related physical couplings of the underlying supergravity theory. Moreover, we elucidate the meaning of the model-dependent coefficients that appear in these expressions: these can be identified with certain topological and arithmetic numbers associated to the singular geometry at the moduli space boundary. We illustrate our findings by studying a wide set of examples.Comment: 100 pages, 6 table

CLINICAL AND CYTOGENETIC FEATURES OF LEUKEMIAS IN CHILDREN TREATED IN THE UNIVERSITY HOSPITAL OF SPLIT FROM 2000 TO 2017

Objectives: Pediatric leukemias are generally characterized by recurrent genetic aberrations, which are thought to be specifically associated with diagnosis and prognosis. The aim of the study was to investigate the frequency and types of acquired chromosomal aberrations and correlation with other biological characteristics and prognostic risk factors. Materials and methods: We retrospectively reviewed clinical features and results of cytogenetics and molecular analysis for patients younger than 18 years with newly diagnosed pediatric leukemia from January 2000 to December 2017. Results: In an 18-year period, 98 children with pediatric leukemia were hospitalized, 47 girls (48 %) and 51 boys (52 %). We had 76 patients diagnosed with ALL (77%), 20 with AML (21%), and 2 with CML (2%). Fever, pallor, lymphadenopathy, and hepatomegaly were the four most common presenting symptoms of leukemia in children (more than 50%). Among all patients, 29% had normal karyotype while 71% had acquired numerical and/or structural chromosomal aberrations. The most frequent chromosomal aberrations in pediatric ALL were t(12;21) ETV6/RUNX1 fusion gene (27%) and hyperdiploidy (15%), both associated with prognostic favorable outcomes and B cell lineage immunophenotype. In AML subgroup, the most frequent chromosomal aberration was translocation t(8;21) with RUNX1-RUNX1T1 fusion gene (21%), slightly higher than reported in the 2008 WHO Classification. On the other hand, the frequency of 11q23 MLL-rearrangements, t(15;17) with PML-RARA fusion gene, inv(16) or del(16q), deletion -7/del(7q) was in accordance to the literature. Two patients were diagnosed with CML, Ph-positive. Conclusion: In this study, the frequency of various acquired chromosomal aberrations as well as their correlation with clinical and biological risk factors in a group of children with newly diagnosed leukemia are similar to previously published studies at pediatric population in Europe and US.Uvod: Pedijatrijske leukemije općenito su karakterizirane ponavljajućim genetičkim aberacijama, a za koje se smatra da su specifično povezane s dijagnozom i prognozom. Cilj istraživanja bio je ispitati učestalost i vrste stečenih kromosomskih aberacija i usporediti ih s drugim biološkim karakteristikama i prognostičkim čimbenicima rizika. Materijali i metode: Retrospektivnim istraživanjem prikazali smo kliničku sliku i rezultate citogenetičke i molekularne analize kod pacijenata mlađih od 18 godina sa novodijagnosticiranom pedijatrijskom leukemijom u periodu od siječnja 2000. do prosinca 2017. godine. Rezultati: U osamnestogodišnjem razdoblju leukemija je dijagnosticiranau 98 djece, 47 djevojčica (48%) i 51 dječaka (52%). Od toga 76 pacijenata imalo je dijagnozu ALL (77%), 20 AML (21%), i 2 CML (2%).Više od 50% djece imalo je četiri najčešća simptoma leukemije:vrućicu, bljedilo, limfadenopatiju i hepatomegaliju.Od svih pacijenata uredan kariotip imalo je 29% pacijenata dok je 71% imalo stečene numeričke i/ili strukturne kromosomske aberacije.Najučestalije aberacije u pedijatrijskoj ALL bile su t(12;21) s fuzijom ETV6/RUNX1 gena (27%) i hiperploidija (15%), a obje su povezane sa prognostički povoljnim ishodom i B staničnim imunofenotipom. U grupi djece sa AML najučestalija kromosomska aberacija bila je t(8;21)s fuzijom gena RUNX1/RUNXT1(21%), nešto viša nego što je objavljeno u klasifikaciji SZO 2008. S druge strane učestalost 11q23 MLL- preuređenja, t(15;17) s fuzijom PML-RARA gena, inv (16) ili del (16q), -7/del(7q) bile su u skladu s podacima iz literature. Philadelphiapozitivnu CML leukemiju imalo je dvoje djece. Zaključak: Učestalost i raznolikost stečenih kromosomskih aberacija upedijatrijskim leukemijama iz našestudijekao i njihova povezanost s kliničkim i biološkim prognostičkim čimbenicima slična je podacima iz literature za pedijatrijsku populaciju u Europi i SAD-u

Modales Netzwerkmodell für die Feldeinkopplung in Verbindungsstrukturen innerhalb von Metallgehäusen mit kleinen Öffnungen

Schnell schaltende elektronische Baugruppen sind häufig in metallischen Gehäusen untergebracht, um diese von äußeren elektromagnetischen Einflüssen abzuschirmen. Ein vollständig geschlossenes Gehäuse ist aus praktischen Gründen nicht realisierbar, da z.B. Öffnungen für Kabeldurchführungen oder Lüftungsgitter erforderlich sind. Dies stellt insbesondere dann ein Problem dar, wenn die Wellenlänge eines externen Feldes in der Größenordnung des Gehäuses liegt. Das durch die Öffnungen eingestrahlte Feld führt in diesem Fall zur Anregung von Hohlraumresonanzen. Um diese Störeinflüsse abzuschätzen, müssen zeitaufwändige Simulationen oder Messungen durchgeführt werden. Eine Analyse im Zeitbereich ist aufgrund der resonanten Struktur zusätzlich erschwert. Für einfache Hohlraumgeometrien können analytische Ansätze basierend auf den Eigenfunktionen bzw. der dyadischen Green’schen Funktion verwendet werden. Für komplexere Problemstellungen sind numerische Methoden wie z.B. Finite-Elemente-Methode geeignet. Aus der Frequenzbereichsanalyse können Systemmodelle abgeleitet werden, die eine Zeitbereichsanalyse mit beliebigen Portabschlüssen ermöglicht. Diese abgeleiteten Systemmodelle, z.B. basierend auf der iterativen Vector-Fitting-Methode [9], sind nicht zwingend stabil im Zeitbereich und können zu unphysikalischen Lösungen führen. Ein kürzlich veröffentlichtes Netzwerkmodell [12] ermöglicht die Analyse von komplexen Verbindungsstrukturen in geschlossenen Metallgehäusen beliebiger Form. Dieses Modell basiert auf den Eigenfunktionen des Systems, die numerisch berechnet werden. Mit einer geeigneten Portdefinition kann die Einkopplung in jeden Mode bestimmt werden, so dass das Systemverhalten durch eine Admittanzdarstellung beschrieben werden kann. Die typischerweise auftretende langsame Konvergenz wird durch die Extraktion des quasistatischen Induktivitäts- und Kapazitätsnetzwerks umgangen, so dass nur so viele Moden berechnet werden müssen, wie zur Analyse bei einer vorgegebenen maximalen Frequenz erforderlich sind. Um den Einfluss von verlustbehafteten Medien zu berücksichtigen, kann das Netzwerkmodell durch modale Widerstände ergänzt werden. Dadurch, dass das resultierende Netzwerkmodell direkt aus den physikalischen Zusammenhängen abgeleitet wird, garantiert es die Stabilität von Zeitbereichsantworten. In diesem Beitrag wird das bereits vorgestellte Modell für geschlossene Gehäuse erweitert, um die Anregung durch externe elektromagnetische Felder berücksichtigen zu können (Abb. 1). Hierbei werden zunächst elektrisch kleine Öffnungen betrachtet. Die Feldverteilung in einer solchen Öffnung kann sehr einfach durch äquivalente Quellen berechnet werden. Außerdem ist der Einfluss der Öffnungen auf die Feldverteilung in dem Gehäuse so gering, dass weiterhin die ungestörten Eigenfunktionen angesetzt werden können. Im folgenden Abschnitt werden zunächst die benötigten äquivalenten Quellen berechnet und anschließend die Integration in das Netzwerkmodell gezeigt. Abschließend wird das erweiterte Modell anhand eines komplexen Beispiels validiert, wobei eine Analyse sowohl im Frequenzbereich als auch im Zeitbereich mit nichtlinearen Lasten erfolgt

Precision Tests of Discrete Symmetries at Low Energies

Low energy precision measurements provide for precise testing of the Standard Model, e.g., in searches for violations of the discrete symmetries charge conjugation (C), parity (P), and time reversal (T) as well as their combinations CP and CPT. We focus here on new experiments concerning atomic parity violation (APV) and searches for a permanent electric dipole moment (EDM) in atoms. In particular, we address precision APV experiments on Ba+ and Ra+ single ions that will enable the extraction of the Weinberg angle at lowest presently accessible momentum transfer. They are expected to contribute towards searches for new particles such as dark Z-bosons. We also review experimental programmes in which an EDM is searched for and we compare them in a common framework. We describe latest EDM searches in heavy effective two-electron atoms such as Xe and Hg. We also indicate possible future prospects of searches for a permanent EDM of the electron using molecules with large enhancement factors

An alternative CYB5A transcript is expressed in aneuploid ALL and enriched in relapse

Background: B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a genetically heterogenous malignancy with poor prognosis in relapsed adult patients. The genetic basis for relapse in aneuploid subtypes such as near haploid (NH) and high hyperdiploid (HeH) BCP-ALL is only poorly understood. Pathogenic genetic alterations remain to be identified. To this end, we investigated the dynamics of genetic alterations in a matched initial diagnosis-relapse (ID-REL) BCP-ALL cohort. Here, we firstly report the identification of the novel genetic alteration CYB5Aalt, an alternative transcript of CYB5A, in two independent cohorts. Methods: We identified CYB5alt in the RNAseq-analysis of a matched ID-REL BCP-ALL cohort with 50 patients and quantified its expression in various molecular BCP-ALL subtypes. Findings were validated in an independent cohort of 140 first diagnosis samples from adult BCP-ALL patients. Derived from patient material, the alternative open reading frame of CYB5Aalt was cloned (pCYB5Aalt) and pCYB5Aalt or the empty vector were stably overexpressed in NALM-6 cells. RNA sequencing was performed of pCYB5Aalt clones and empty vector controls followed by differential expression analysis, gene set enrichment analysis and complementing cell death and viability assays to determine functional implications of CYB5Aalt. Results: RNAseq data analysis revealed non-canonical exon usage of CYB5Aalt starting from a previously undescribed transcription start site. CYB5Aalt expression was increased in relapsed BCP-ALL and its occurrence was specific towards the shared gene expression cluster of NH and HeH BCP-ALL in independent cohorts. Overexpression of pCYB5Aalt in NALM-6 cells induced a distinct transcriptional program compared to empty vector controls with downregulation of pathways related to reported functions of CYB5A wildtype. Interestingly, CYB5A wildtype expression was decreased in CYB5Aalt samples in silico and in vitro. Additionally, pCYB5Aalt NALM-6 elicited a more resistant drug response. Conclusions: Across all age groups, CYB5Aalt was the most frequent secondary genetic event in relapsed NH and HeH BCP-ALL. In addition to its high subgroup specificity, CYB5Aalt is a novel candidate to be potentially implicated in therapy resistance in NH and HeH BCP-ALL. This is underlined by overexpressing CYB5Aalt providing first evidence for a functional role in BCL2-mediated apoptosis

A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer

Although microRNAs (miRNAs) contribute to all hallmarks of cancer, miRNA dysregulation in metastasis remains poorly understood. The aim of this work was to reliably identify miRNAs associated with metastatic progression of colorectal cancer (CRC) using novel and previously published nextgeneration sequencing (NGS) datasets generated from 268 samples of primary (pCRC) and metastatic CRC (mCRC; liver, lung and peritoneal metastases) and tumor adjacent tissues. Differential expression analysis was performed using a meticulous bioinformatics pipeline, including only bona fide miRNAs, and utilizing miRNA-tailored quality control and processing. Five miRNAs were identified as upregulated at multiple metastatic sites Mir-210 3p, Mir191 5p, Mir-8-P1b 3p [mir-141–3p], Mir-1307 5p and Mir-155 5p. Several have previously been implicated in metastasis through involvement in epithelial-tomesenchymal transition and hypoxia, while other identified miRNAs represent novel findings. The use of a publicly available pipeline facilitates reproducibility and allows new datasets to be added as they become available. The set of miRNAs identified here provides a reliable starting-point for further research into the role of miRNAs in metastatic progression

Isocitrate dehydrogenase 1 mutation drives leukemogenesis by PDGFRA activation due to insulator disruption in acute myeloid leukemia (AML)

Acute myeloid leukemia (AML) is characterized by complex molecular alterations and driver mutations. Elderly patients show increased frequencies of IDH mutations with high chemoresistance and relapse rates despite recent therapeutic advances. Besides being associated with global promoter hypermethylation, IDH1 mutation facilitated changes in 3D DNA-conformation by CTCF-anchor methylation and upregulated oncogene expression in glioma, correlating with poor prognosis. Here, we investigated the role of IDH1 p.R132H mutation in altering 3D DNA-architecture and subsequent oncogene activation in AML. Using public RNA-Seq data, we identified upregulation of tyrosine kinase PDGFRA in IDH1-mutant patients, correlating with poor prognosis. DNA methylation analysis identified CpG hypermethylation within a CTCF-anchor upstream of PDGFRA in IDH1-mutant patients. Increased PDGFRA expression, PDGFRA-CTCF methylation and decreased CTCF binding were confirmed in AML CRISPR cells with heterozygous IDH1 p.R132H mutation and upon exogenous 2-HG treatment. IDH1-mutant cells showed higher sensitivity to tyrosine kinase inhibitor dasatinib, which was supported by reduced blast count in a patient with refractory IDH1-mutant AML after dasatinib treatment. Our data illustrate that IDH1 p.R132H mutation leads to CTCF hypermethylation, disrupting DNA-looping and insulation of PDGFRA, resulting in PDGFRA upregulation in IDH1-mutant AML. Treatment with dasatinib may offer a novel treatment strategy for IDH1-mutant AML