Caratterizzazione Citogenetico-Molecolare delle alterazioni cromosomiche 3q26 e 1p36 nelle Sindromi Mieloproliferative

L’overespressione dei geni EVI1(3q26) e PRDM16(1p36), è descritta sia in presenza che in assenza di riarrangiamenti 3q26 e 1p36 in specifici sottogruppi citogenetici di LAM, ed è associata ad una prognosi sfavorevole. Lo scopo principale del nostro studio è stato identificare e caratterizzare tramite FISH e RQ-PCR, alterazioni di EVI1 e PRDM16 in pazienti con alterazioni cromosomiche 3q e 1p.Riarrangiamenti di EVI1 si associavano ad alterazioni cromosomiche 3q26, ma, in 6 casi (6/35;17,1%) erano presenti in assenza di coinvolgimenti, in citogenetica convenzionale, della regione 3q26, a causa di meccanismi complessi e/o alterazioni ‘criptiche’. Inoltre, abbiamo identificato quattro nuovi riarrangiamenti di EVI1, tra cui due nuove traslocazioni simili presenti in due fratelli. Riarrangiamenti e/o amplificazioni di PRDM16 erano spesso associate ad alterazioni 1p36 (7/14;50%). L’analisi di EVI1 e PRDM16 è stata estesa ad altri casi con alterazioni -7/7q-, con cariotipo normale, con alterazioni 3q per PRDM16 e con alterazioni 1p per EVI1. L’overespressione di EVI1 era presente solo nel gruppo -7/7q- (10/58;17.2%) ed in un caso si associava ad amplificazione genica, mentre PRDM16 era overespresso in casi di tutti i gruppi analizzati,sia con cariotipi complessi, dove si associava in alcuni casi ad amplificazione genica, sia con cariotipi normali o con singole alterazioni. Il nostro studio dimostra come la FISH permetta di identificare alterazioni dei geni EVI1 e PRDM16, anche in assenza di coinvolgimenti delle regioni 3q26 e 1p36. Riarrangiamenti complessi e/o una scarsa qualità dei preparati citogenetici sono le cause principali per la mancata identificazione di queste alterazioni. La RQ-PCR permette di identificare l’overespressione anche nei casi in cui non sia dovuta ad alterazioni citogenetiche. È importante confermare con FISH e/o RQ-PCR il coinvolgimento di questi due geni, per individuare alla diagnosi pazienti con prognosi sfavorevole e che potranno beneficiare di terapie maggiormente aggressive e/o di trapianto allogenico di cellule staminali.

Caratterizzazione citogenetico-molecolare alla diagnosi di pazienti con leucemia mieloide cronica in fase cronica trattati con inibitori delle tirosinchinasi: ruolo prognostico.

L’applicazione della citogenetica convenzionale e molecolare può identificare: Ph-negatività, traslocazioni t(9;22) varianti e alterazioni citogenetiche addizionali (ACA) al cromsoma Ph in pazienti con LMC alla diagnosi. Prima dell’introduzione della terapia con Imatinib, esse mostravano un impatto prognostico negativo o non chiaro. Nel nostro studio, 6 casi di LMC Ph- erano trattati con Imatinib. La FISH identificava 4 casi con riarrangiamento BCR/ABL sul der(9q), 1 sul der(22q) e 1 su entrambi i derivativi. Quattro pazienti (66,7%) raggiungevano la RCgC, 2 fallivano il trattamento e 1 sottoposto a TMO. A causa dello scarso numero di casi, non era possibile nessuna correlazione con la prognosi. Nell’ambito di studi prospettici multicentrici del GIMEMA-WP, abbiamo valutato: traslocazioni varianti e ACA. Dei 559 pazienti arruolati, 30(5%) mostravano traslocazioni varianti, 24 valutabili in FISH: 18(75%) mostravano meccanismo 1-step, 4(16,7%) meccanismo 2-step e 2(8,3%) meccanismo complesso. Abbiamo confermato che le varianti non influenzano la risposta e la sopravvivenza dei pazienti trattati con Imatinib. Dei 378 pazienti valutabili alla diagnosi con citogenetica convenzionale, 21(5,6%) mostravano ACA: 9(43%) avevano la perdita del cromosoma Y, 3(14%) trisomia 8, 2(10%) trisomia 19, 6(28%) altre singole anomalie e 1 cariotipo complesso. La presenza di ACA influenzava la risposta: le RCgC e RMolM erano significativamente più basse rispetto al gruppo senza ACA e le curve di sopravvivenza EFS e FFS non erano significativamente diverse. Le curve di PFS e OS erano sovrapponibili nei due gruppi, per il basso numero di eventi avversi oppure perché alcuni raggiungevano la risposta con TKI di seconda generazione. Le anomalie “major route” mostravano decorso clinico peggiore, ma non è stato possibile determinare l’impatto prognostico in relazione al tipo di alterazione. Pertanto, le ACAs alla diagnosi rivestono un ruolo negativo nella prognosi dei pazienti trattati con Imatinib, che quindi rappresentano una categoria più a rischio per la risposta.

Caratterizzazione biomolecolare delle neoplasie lipomatose

Tra i liposarcomi, il tumore lipomatoso atipico/liposarcoma ben differenziato e il liposarcoma dedifferenziato rappresentano i sottotipi più frequenti. Spesso è difficile distinguere questi tumori da altri con caratteristiche morfologiche simili. Da un punto di vista citogenetico sono caratterizzati dalla presenza di cromosomi soprannumerari giganti e cromosomi ad anello costituiti principalmente da sequenze amplificate della regione 12q13-15. In questa regione mappano numerosi geni tra cui il gene MDM2 (murine double minute-2). La caratterizzazione molecolare di tali sottotipi diventa estremamente importante sia a fini diagnostici sia per un corretto indirizzo terapeutico, soprattutto oggi, dopo l’introduzione nella pratica clinica di terapie biologiche mirate (targeted therapies). Nel presente studio viene analizzato il ruolo dell’analisi FISH per la valutazione dello status di MDM2 nelle neoplasie lipomatose e per stabilire se questo marcatore possa essere utilizzato nella diagnosi differenziale di questi tumori. Sebbene questo studio confermi l’utilità diagnostica dell’amplificazione di MDM2 nella diagnosi del tumore lipomatoso atipico/liposarcoma ben differenziato ed il liposarcoma dedifferenziato, questo marcatore potrebbe avere in futuro anche una più ampia applicazione. Data la recente introduzione degli inibitori selettivi di MDM2 tale ricerca risulta importante non solo a fini diagnostici ma anche per la selezione dei pazienti che potranno in futuro beneficiare del trattamento con tali inibitori. Questo studio è stato effettuato anche per analizzare la rilevanza biologica del percorso che vede coinvolto il gene AKT nel liposarcoma ben differenziato e dedifferenziato e per stabilire se questo percorso possa rappresentare un utile bersaglio terapeutico in questi tumori. I dati ottenuti dimostrano che AKT è espresso ed attivato in tutti i casi di tumore lipomatoso atipico/liposarcoma ben differenziato e liposarcoma dedifferenziato.

Untersuchungen zum Engraftment primärer humaner akuter myeloischer Leukämieblasten in einem immundefizienten Mausmodel

Die akute myeloische Leukämie (AML) stellt ein äußerst heterogenes hämatologisches Krankheitsbild dar, welches durch die unkontrollierte Proliferation unausdifferenzierter und gleichzeitig nicht-funktioneller hämatopoetischer Zellen gekennzeichnet ist. Sowohl die unterschiedliche Zellherkunft, als auch zytogenetische Aberrationen und molekulargenetische Mutationen sorgen für eine große Diversität der Erkrankung. In der Therapie kommen Chemotherapeutika zum Einsatz, welche die Leukämie in eine komplette Remission bringen sollen. Der einzige kurative Ansatz besteht aus der allogenen hämatopoetischen Stammzelltransplantation. Abgesehen von den gewünschten kurativen Effekten, induzieren die im Transplantat befindlichen Spender-T-Lymphozyten ebenfalls die Transplantat-gegen-Wirt Erkrankung – eine Hauptursache von Mortalität und Morbidität nach erfolgter allogener hämatopoetischer Stammzelltransplantation. Da bei vielen Patienten aufgrund ihres Alters und ihrer Begleiterkrankungen eine Transplantation nicht tolerieren und da viele akuten myeloischen Leukämien trotz Chemotherapie progredient sind, schlägt die Therapie fehl und es gibt keine Chance auf Heilung. rnZur Erforschung der pathologischen Prozesse der akuten myeloischen Leukämie sowie für die Entwicklung neuer Therapiekonzepte bedarf es stabiler Tiermodelle, die die maligne Erkrankung des Menschen darstellen können. Ziel der vorliegenden Arbeit war die Untersuchung des Engraftments humaner primärer akuter myeloischer Leukämien in immuninkompetenten NSG-Mäusen. Die Untersuchungen zeigten, dass lediglich 61,5% der getesteten Leukämien in den Versuchstieren nach der Xenotransplantation nachgewiesen werden konnten. Die Gründe hierfür sind noch nicht ausreichend geklärt, beinhalten jedoch vermutlich Elemente des Homings, des Überlebens der Zelle in der fremden murinen Knochenmarknische, der Abwesenheit spezifischer humaner Wachstumsfaktoren, sowie intrinsische Unterschiede unter den verschiedenen Leukämieproben. Leukämien, die mit einer schlechten Prognose beim Patienten verbunden sind, wachsen in den Tieren stärker an. In den Versuchen konnte gezeigt werden, dass Leukämien mit einer Längenmutation des FLT3-Rezeptors eher häufiger in den NSG-Mäusen anwachsen, als wenn diese Mutation fehlt. Die Analyse der erstellten Wachstumskinetiken zweier Leukämien ergab, dass die Höhe des Engraftments in den einzelnen Organen sowohl von der transplantierten Zellmenge, als auch von der Höhe der angesetzten Versuchszeit abhängt. Zudem wurde ein Wachstum humaner T-Lymphozyten in den xenotransplantierten Mäusen beobachtet, welches sowohl mit einem höheren Engraftment der Leukämie in der Maus verbunden war, als auch mit einer höheren Tiersterblichkeit vergesellschaftet war.rnZum Verhindern dieses Wachstums wurden zwei unterschiedliche Methoden angewendet und miteinander verglichen. Dabei erzielten sowohl die medikamentöse Behandlung der Tiere mit dem Calcineurininhibitor Cyclosporin A, als auch die CD3-Depletion der Leukämie vor der Transplantation ein T-Zell-freies Wachstum in den Mäusen, letzteres erwies sich jedoch als das schonendere Verfahren. In den T-Zell-freien Tieren konnte bei dem Großteil der Tiere kein Engraftment im Knochenmark festgestellt werden, was auf einen positiven Einfluss der humanen T-Lymphozyten beim Vorgang des Engraftments schließen lässt.rn

Identification of novel genetic alterations in pediatric cytogenetically normal acute myeloid leukemia by next-generation sequencing

Pediatric acute myeloid leukemia (AML) is a molecularly heterogeneous disease that arises from genetic alterations in pathways that regulate self-renewal and myeloid differentiation. While the majority of patients carry recurrent chromosomal translocations, almost 20% of childhood AML do not show any recognizable cytogenetic alteration and are defined as cytogenetically normal (CN)-AML. CN-AML patients have always showed a great variability in response to therapy and overall outcome, underlining the presence of unknown genetic changes, not detectable by conventional analyses, but relevant for pathogenesis, and outcome of AML. The development of novel genome-wide techniques such as next-generation sequencing, have tremendously improved our ability to interrogate the cancer genome. Based on this background, the aim of this research study was to investigate the mutational landscape of pediatric CN-AML patients negative for all the currently known somatic mutations reported in AML through whole-transcriptome sequencing (RNA-seq). RNA-seq performed on diagnostic leukemic blasts from 19 pediatric CN-AML cases revealed a considerable incidence of cryptic chromosomal rearrangements, with the identification of 21 putative fusion genes. Several of the fusion genes that were identified in this study are recurrent and might have a prognostic and/or therapeutic relevance. A paradigm of that is the CBFA2T3-GLIS2 fusion, which has been demonstrated to be a common alteration in pediatric CN-AML, predicting poor outcome. Important findings have been also obtained in the identification of novel therapeutic targets. On one side, the identification of NUP98-JARID1A fusion suggests the use of disulfiram; on the other, here we describe alteration-activating tyrosine kinases, providing functional data supporting the use of tyrosine kinase inhibitors to specifically inhibit leukemia cells. This study provides new insights in the knowledge of genetic alterations underlying pediatric AML, defines novel prognostic markers and putative therapeutic targets, and prospectively ensures a correct risk stratification and risk-adapted therapy also for the “all-neg” AML subgroup.

Integrating novel agents into multiple myeloma treatment - current status in Switzerland and treatment recommendations

The treatment of multiple myeloma has undergone significant changes in the recent past. The arrival of novel agents, especially thalidomide, bortezomib and lenalidomide, has expanded treatment options and patient outcomes are improving significantly. This article summarises the discussions of an expert meeting which was held to debate current treatment practices for multiple myeloma in Switzerland concerning the role of the novel agents and to provide recommendations for their use in different treatment stages based on currently available clinical data. Novel agent combinations for the treatment of newly diagnosed, as well as relapsed multiple myeloma are examined. In addition, the role of novel agents in patients with cytogenetic abnormalities and renal impairment, as well as the management of the most frequent side effects of the novel agents are discussed. The aim of this article is to assist in treatment decisions in daily clinical practice to achieve the best possible outcome for patients with multiple myeloma.

Sequence analysis of the porcine IFNAR1 and IFNGR2 genes

A porcine BAC clone harboring the tightly linked IFNAR1 and IFNGR2 genes was identified by comparative analysis of the publicly available porcine BAC end sequences. The complete 168,835 bp insert sequence of this clone was determined. Sequence comparisons of the genomic sequence with EST sequences from public databases were performed and allowed a detailed annotation of the IFNAR1 and IFNGR2 genes. The analyzed genes showed a conserved genomic organization with their known mammalian orthologs, however the sequence conservation of these genes across species was relatively low. In addition to the IFNAR1 and IFNGR2 genes, which were completely sequenced, the analyzed BAC clone also contained parts of an orphan gene encoding a putative transmembrane protein (TMEM50B). In contrast to the IFNAR1 and IFNGR2 genes the sequence conservation of the TMEM50B gene across different mammalian species was extremely high.

The bovine aristaless-like homeobox 4 (ALX4) as a candidate gene for syndactyly

The ALX4 (aristaless-like homeobox 4) gene encodes a paired-type homeodomain transcriptional activator and plays a major role in anterior-posterior pattern formation during limb development. Here, the cloning, genomic structure and expression of the bovine ortholog of the ALX4 gene are reported. The bovine ALX4 gene consists of four exons and is located on BTA15q28-->q29 in a region syntenic to HSA11p11.2. The transcribed ALX4 mRNA encodes a 397-amino-acid protein showing a paired-type homeodomain and a C-terminal stretch of amino acids known as the OAR- or aristaless domain. The predicted protein shares 92.5% identity to human and mouse ALX4 proteins and all three species share almost complete identity in the conserved domains. ALX4 expression was detected by reverse transcriptase polymerase chain reaction in bovine fetal limb bones. The ALX4 gene was evaluated as a candidate gene for bovine syndactyly which has been mapped on the telomeric region of cattle chromosome 15. Sequencing of the four exons with flanking sequences of the bovine ALX4 gene from a panel of 14 affected animals belonging to German Holstein, German Fleckvieh and crossbreds, and 27 unaffected individuals from German Holstein revealed five silent SNPs within the coding region out of eleven SNPs in total. Four SNPs were polymorphic in the affected animals, but in comparison to the genotyped unaffected individuals the genotype distribution showed no evidence for an association to the phenotype. Therefore our data indicate that the ALX4 gene can probably be excluded as candidate gene for bovine syndactyly in the examined animals.

Molecular characterization of the equine collagen, type IX, alpha 2 (COL9A2) gene on horse chromosome 2p16-->p15

The mammalian collagen, type IX, alpha 2 gene (COL9A2) encodes the alpha-2 chain of type IX collagen and is located on horse chromosome 2p16-->p14 harbouring a quantitative trait locus for osteochondrosis. We isolated a bacterial artificial chromosome (BAC) clone containing the equine COL9A2 gene and determined the complete genomic sequence of this gene. Cloning and characterization of equine COL9A2 revealed that the equine gene consists of 32 exons spanning approximately 15 kb. The COL9A2 transcript encodes a single protein of 688 amino acids. Thirty two single nucleotide polymorphisms (SNPs) equally distributed in the gene were detected in a mutation scan of eight unrelated Hanoverian warmblood stallions, including one SNP that affects the amino acid sequence of COL9A2. Comparative analyses between horse, human, mouse and rat indicate that the chromosomal location of equine COL9A2 is in agreement with known chromosomal synteny relationships. The comparison of the gene structure and transcript revealed a high degree of conservation towards the other mammalian COL9A2 genes. We chose three informative SNPs for association and linkage disequilibrium tests in three to five paternal half-sib families of Hanoverian warmblood horses consisting of 44 to 75 genotyped animals. The test statistics did not reach the significance threshold of 5% and so we could not show an association of COL9A2 with equine osteochondrosis.

Cytogenetics of pineoblastoma: four new cases and a literature review

Pineoblastoma represents a class of primitive neuroectodermal tumors (PNET) with poorly differentiated neuroepithelial cells that are histologically indistinguishable from medulloblastomas. It is a rare tumor, typically arising in childhood, and to date only a few cytogenetic cases have been published. We report four new cases in which conventional cytogenetics demonstrated the presence of an abnormal clone. The tumors showed a variety of ploidy levels, from hypodiploid to hypertetraploid. Both structural and numerical aberrations were frequent, and in three out of the four cases a large degree of cell-to-cell variation was observed. The most frequently involved chromosome in structural rearrangements was chromosome 1, observed in three of the four cases. The short arm was involved in two of the three cases; in the third case, the anomaly was in the long arm. Two cases showed unbalanced gain of chromosome 17q, one of them showing i(17)(q10). Together, the four cases illustrate the complex karyotypic nature of this tumor type and represent a step toward determining whether a nonrandom cytogenetic picture exists and how this may be related to other associated tumor types.

FISH mapping of 10 canine BAC clones harbouring genes and microsatellites in the arctic fox and the Chinese raccoon dog genomes

Cytogenetic mapping of the arctic fox and the Chinese raccoon dog were performed using a set of canine probes derived from the Bacterial Artificial Chromosome (BAC) library. Altogether, 10 BAC clones containing sequences of selected genes (PAX3, HBB, ATP2A2, TECTA, PIT1, ABCA4, ESR2, TPH1, HTR2A, MAOA) and microsatellites were mapped by fluorescence in situ hybridization (FISH) experiments to chromosomes of the canids studied. At present, the cytogenetic map on the arctic fox and Chinese raccoon dog consists of 45 loci each. Chromosomal localization of the BAC clones was in agreement with data obtained by earlier independent comparative chromosome painting. However, two events of telomere-to-centromere inversions were tentatively identified while compared with assignments in the dog karyotype.

A radiation hybrid map of sheep chromosome 23 based on ovine BAC-end sequences

More than 375,000 BAC-end sequences (BES) of the CHORI-243 ovine BAC library have been deposited in public databases. blastn searches with these BES against HSA18 revealed 1806 unique and significant hits. We used blastn-anchored BES for an in silico prediction of gene content and chromosome assignment of comparatively mapped ovine BAC clones. Ovine BES were selected at approximately 1.3-Mb intervals of HSA18 and incorporated into a human-sheep comparative map. An ovine 5000-rad whole-genome radiation hybrid panel (USUoRH5000) was typed with 70 markers, all of which mapped to OAR23. The resulting OAR23 RH map included 43 markers derived from BES with high and unique BLAST hits to the sequence of the orthologous HSA18, nine EST-derived markers, 16 microsatellite markers taken from the ovine linkage map and two bovine microsatellite markers. Six new microsatellite markers derived from the 43 mapped BES and the two bovine microsatellite markers were linkage-mapped using the International Mapping Flock (IMF). Thirteen additional microsatellite markers were derived from other ovine BES with high and unique BLAST hits to the sequence of the orthologous HSA18 and also positioned on the ovine linkage map but not incorporated into the OAR23 RH map. This resulted in 24 markers in common and in the same order between the RH and linkage maps. Eight of the BES-derived markers were mapped using fluorescent in situ hybridization (FISH), to thereby align the RH and cytogenetic maps. Comparison of the ovine chromosome 23 RH map with the HSA18 map identified and localized three major breakpoints between HSA18 and OAR23. The positions of these breakpoints were equivalent to those previously shown for syntenic BTA24 and HSA18. This study presents evidence for the usefulness of ovine BES when constructing a high-resolution comprehensive map for a single sheep chromosome. The comparative analysis confirms and refines knowledge about chromosomal conservation and rearrangements between sheep, cattle and human. The constructed RH map demonstrates the resolution and utility of the newly constructed ovine RH panel.

Losses of chromosome arms 4q, 8p, 13q and gain of 8q are correlated with increasing chromosomal instability in hepatocellular carcinoma

OBJECTIVE: Chromosomal instability is a key feature in hepatocellular carcinoma (HCC). Array comparative genomic hybridization (aCGH) revealed recurring structural aberrations, whereas fluorescence in situ hybridization (FISH) indicated an increasing number of numerical aberrations in dedifferentiating HCC. Therefore, we examined whether there was a correlation between structural and numerical aberrations of chromosomal instability in HCC. METHODS AND RESULTS: 27 HCC (5 well, 10 moderately, 12 lower differentiated) already cytogenetically characterized by aCGH were analyzed. FISH analysis using probes for chromosomes 1, 3, 7, 8 and 17 revealed 1.46-4.24 signals/nucleus, which correlated with the histological grade (well vs. moderately,p < 0.0003; moderately vs. lower, p < 0.004). The number of chromosomes to each other was stable with exceptions only seen for chromosome 8. Loss of 4q and 13q, respectively, were correlated with the number of aberrations detected by aCGH (p < 0.001, p < 0.005; Mann-Whitney test). Loss of 4q and gain of 8q were correlated with an increasing number of numerical aberrations detected by FISH (p < 0.020, p < 0.031). Loss of 8p was correlated with the number of structural imbalances seen in aCGH (p < 0.048), but not with the number of numerical changes seen in FISH. CONCLUSION: We found that losses of 4q, 8p and 13q were closely correlated with an increasing number of aberrations detected by aCGH, whereas a loss of 4q and a gain of 8q were also observed in the context of polyploidization, the cytogenetic correlate of morphological dedifferentiation.

Non-classical karyotypic features in relapsed childhood B-cell precursor acute lymphoblastic leukemia

Karyotype analysis of acute lymphoblastic leukemia (ALL) at diagnosis has provided valuable prognostic markers for treatment stratification. However, reports of cytogenetic studies of relapsed ALL samples are limited. We compared the karyotypes from 436 nonselected B-cell precursor ALL patients at initial diagnosis and of 76 patients at first relapse. We noticed a relative increase of karyotypes that did not fall into the classic ALL cytogenetic subgroups (high hyperdiploidy, t(12;21), t(9;22), 11q23, t(1;19), <45 chromosomes) in a group of 29 patients at relapse (38%) compared to 130 patients at presentation (30%). Non-classical cytogenetic aberrations in these 29 patients were mostly found on chromosomes 1, 2, 7, 9, 13, 14, and 17. We also describe six rare reciprocal translocations, three of which involved 14q32. The most frequent abnormalities were found in 9p (12/29 cases) and were associated with a marked decrease in the duration of the second remission, but not of the probability of 10-year event-free survival after relapse treatment. From 29 patients with non-classical cytogenetic aberrations, only 8 (28%) had been stratified to a high risk-arm on the first treatment protocol, suggesting that this subgroup might benefit from the identification of new prognostic markers in future studies.