Acute lymphoblastic leukemia (ALL) is the most frequent malignancy in childhood and adolescence. In more than 60% of cases of this heterogeneous disease, a genetic marker is identified via cytogenetic or molecular analyses. TCF3 gene fusions occur in 5%–11% of ALL patients. In < 1%, the TCF3 alteration in ALL leads to a TCF3‐HLF fusion gene. Even though this is a very rare event, the detection of a TCF3‐HLF fusion gene is associated with a very poor prognosis with incurable relapses in almost all patients. The frequent TCF3‐PBX1 fusion gene, which is detectable in 5%–10% of childhood B‐cell precursor ALLs and ~3.8% of adult B‐cell precursor ALLs, is associated with a rather good prognosis, that is, an observed event‐free 5‐year survival of approximately 85%. Thus, the distinction of the different partner genes fused to TCF3 is essential for risk assessment. To verify RNA sequencing as a tool for detection of known and unknown fusion genes, we screened 200 cases of pediatric B‐cell precursor ALL with “targeted” RNA sequencing in a pilot project in comparison to classical cytogenetic analyses (chromosome R‐banding analysis), fluorescence in situ hybridization, and PCR. We observed a TCF3 fusion gene in 6.5% (13/200) of the patients. Ten (5%) patients displayed a TCF3‐PBX1 fusion gene, two (1%) patients a TCF3‐FLI1 fusion gene, and one (0.5%) patient a TCF3‐HLF fusion gene. For the TCF3 fusions, we obtained discrepant results with the different methods, which are described in the article. Taken together, translocations leading to TCF3 fusion genes might appear cryptic and may remain undetected by a single method.

Risk-adapted therapy has significantly contributed to improved survival rates in pediatric acute lymphoblastic leukemia (ALL) and reliable detection of chromosomal aberrations is mandatory for risk group stratification. This study evaluated the applicability of panel-based RNA sequencing and array CGH within the diagnostic workflow of the German study group of the international AIEOP-BFM ALL 2017 trial. In a consecutive cohort of 117 children with B cell precursor (BCP) ALL, array analysis identified twelve cases with an IKZF1(plus) profile of gene deletions and one case of masked hypodiploidy. Genetic markers BCR-ABL1 (n = 1), ETV6-RUNX1 (n = 25), and rearrangements involving KMT2A (n = 3) or TCF3 (n = 3) were assessed by established conventional techniques such as karyotyping, FISH, and RT-PCR. Comparison of these results with RNA sequencing analysis revealed overall consistency in n=115/117 cases, albeit with one undetected AFF1-KMT2A fusion in RNA sequencing and one undetected ETV6-RUNX1 fusion in conventional analyses. The combined application of RNA sequencing, FISH, and CGH+SNP array reliably detected all genetic markers necessary for risk stratification and will be used as the diagnostic standard workflow for BCP-ALL patients enrolled in the AIEOP-BFM ALL 2017 study. Prospectively, consistent collection of genome-wide CGH+SNP array as well as RNA sequencing data will be a valuable source to elucidate new prognostic lesions beyond established markers of pediatric ALL. In this respect, RNA sequencing identified various gene fusions in up to half of the IKZF1(plus) (n = 6/12) and B-other (n = 19/36) cases but not in cases with hyperdiploid karyotypes (n = 35). Among these fusions, this study reports several previously undescribed in frame PAX5 fusions, including PAX5-MYO1G and PAX5-NCOA6.

Chromosomal rearrangements involving one donor chromosome and two or more recipient chromosomes are called jumping translocations. To date only few cases of acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) with jumping translocations have been described and the underlying mechanisms remain unclear. Here, we analyzed 11 AML and 5 MDS cases with jumping translocations. The cases were analyzed by karyotyping, FISH, telomere length measurement, and next-generation sequencing with an AML/MDS gene panel. Cases with jumping translocations showed significantly (P < .01) shorter telomeres in comparison to healthy age-matched controls. Additional neo-telomeres were found in two cases. In total, eight cases showed recipient chromosomes with a breakpoint in the centromeric region all of them harboring a pathogenic variant in the TP53 gene (n = 6) and/or a loss of TP53 (n = 5). By contrast, no pathogenic variant or loss of TP53 was identified in the six cases showing recipient chromosomes with a breakpoint in the telomeric region. In conclusion, our results divide the cohort of AML and MDS cases with jumping translocations into two groups: the first group with a telomeric breakpoint of the recipient chromosome is characterized by short telomeres and a possibly telomere-based mechanism of chromosomal instability formation. The second group with a centromeric breakpoint of the recipient chromosome is defined by mutation and/or loss of TP53. We, therefore, assume that both critically short telomeres as well as pathogenic variants of TP53 influence jumping translocation formation.

CMML is an aggressive form of myeloid neoplasia with features of myelodysplastic/myeloproliferative neoplasm (MDS/MPN) characterized by peripheral monocytosis and bone marrow dysplasia. Therapeutic options are limited. Median survival is 24 months [1]. The prognostic risk score comprises the variables BM blasts, WBC count, RBC transfusion dependency as well as the genetic risk groups. The latter is categorized according to the cytogenetic risk group as well as mutational status of ASXL1, NRAS, RUNX1 and SETBP1 [2]. Acute myeloid leukaemia (AML) arising from chronic myelomonocytic leukaemia (CMML) is usually associated with a poor prognosis and occurs in 10–30% of cases [3,4]. Around 55% of these transformed cases, show a normal karyotype and a pathogenic NPM1 variant can be detected in 17%. Median survival is 6 months, and with this, similar to AML secondary to MDS [3]. Karyotypic abnormalities characteristically comprise AML-associated aberrations including trisomy 8, monosomy 7, deletions of part of the long arm of chromosome 7, structural abnormalities of the short arm of chromosome 12 and complex karyotypes [4]. We, here, describe a 72-year-old-male patient who was diagnosed with a cytogenetically normal CMML-1. No molecular genetic analyzes were performed at first diagnosis. He was treated with G-CSF and erythropoietin. Cytogenetic analysis on blood cells still showed a normal karyotype. The pathogenic JAK2 variant c.1849G> T; p.V617F was positive. At the age of 80 years (99 months after initial diagnosis), a secondary AML was diagnosed. The blast count was 60% with early myeloid differentiation and multilineage dysplasia. At that time a hyperdiploid karyotype with—among other numerical aberrations—an octasomy of the chromosome 21 was detected (54,XY,þ13,þ19,þ21,þ21,þ21,þ21,þ21,þ21[14]/ 46,XY[1]) (Figure 1(A)). Treatment with azacitidine was started, but he died 2 months after the diagnosis of secondary AML (101 months after initial diagnosis of CMML). In addition to our case, we found one case of secondary AML and a hyperdiploid karyotype (trisomy 13 and 15) after a cytogenetically normal CMML with an overall survival of 5 months after diagnosis of AML he had a particularly poor outcome [4]. The patient from that case report survived for additional 2 months after diagnosis of a secondary AML. With respect to that case, and the disease history of our patient with an octasomy 21, we speculate that these karyotypic abnormalities are associated with an extremely adverse outcome. Keeping in mind, that AML with an aneuploidy of chromosome 21 or chromosome 8 is generally associated with an intermediate prognosis [5], larger studies will have to shed light on this speculation that will have impact for the patients. Furthermore, the detection of octasomy of chromosome 21 raised the question of the potential genetic trigger of this the very rare cytogenetic aberration during progression of the disease. As RUNX1 is located on chromosome 21. RUNX1 mutations are prognostically relevant in myeloid leukemia and are causative for a subtype of familial leukemia. It was our interest to investigate this patient on the genetic level [6]. We, therefore, performed retrospective analysis of the patient via array CGH analysis and a mutational hotspot analysis using the Illumina TruSight Myeloid Sequencing Panel (Illumina, San Diego, CA). Mutational hotspot analysis could be performed on DNA from bone marrow cells obtained after stimulated cell culture 64 months after initial diagnosis as well as on DNA from fresh bone marrow cells 99 months after initial diagnosis. Unfortunately, this was not possible at the time point of diagnosis because of low DNA quality. Array CGH analysis could only be performed on material of the last time point (Supplementary data). NGS panel analysis during the course of the CMML revealed the known pathogenic variant in JAK2 and three further pathogenic variants in TET2 [c.5618T>C;

TP53 deficiencies characterize myeloid malignancies with a dismal prognosis. To unravel the pathomechanism of TP53 mutations in the development of myeloid malignancies, we analyzed the functional properties of TP53 conformational and contact mutations and TP53 loss in human CD34+ cells. We show for the first time that the analyzed conformational mutations lead to higher cell viability in human hematopoietic stem progenitor cells. In contrast to these conformational mutations, contact mutations interfered with efficient erythropoiesis. These findings show that not only the detection of a TP53 mutation is important, but also the specific mutation may play a role in malignant transformation and progression.

Myelodysplastic syndrome (MDS) can easily transform into acute myeloid leukemia (AML), a process which is often associated with clonal evolution and development of complex karyotypes. Deletion of 5q (del(5q)) is the most frequent aberration in complex karyotypes. This prompted us to analyze clonal evolution in MDS patients with del(5q). There were 1684 patients with low and intermediate-risk MDS and del(5q) with or without one additional cytogenetic abnormality, who were investigated cytogenetically in our department, involving standard karyotyping, fluorescence in situ hybridization (FISH) and multicolor FISH. We identified 134 patients (8%) with aspects of clonal evolution. There are two main routes of cytogenetic clonal evolution: a stepwise accumulation of cytogenetic events over time and a catastrophic event, which we defined as the occurrence of two or more aberrations present at the same time, leading to a sudden development of highly complex clones. Of the 134 patients, 61% underwent a stepwise accumulation of events whereas 39% displayed a catastrophic event. Patients with isolated del(5q) showed significantly more often a stepwise accumulation of events rather than a catastrophic event. The most frequent aberrations in the group of stepwise accumulation were trisomy 8 and trisomy 21 which were significantly more frequent in this group compared to the catastrophic event group. In the group with catastrophic events, del(7q)/-7 and del(17p)/-17 were the most common aberrations. A loss of 17p, containing the tumor suppressor gene TP53, was found significantly more frequent in this group compared to the group of stepwise accumulation. This leads to the assumption that the loss of TP53 is the driving force in patients with del(5q) who undergo a sudden catastrophic event and evolve into complex karyotypes.

RATIONALE:Although the transplantation of induced pluripotent stem cell (iPSC)-derived cells harbors enormous potential for the treatment of pulmonary diseases, in vivo data demonstrating clear therapeutic benefits of human iPSC-derived cells in lung disease models are missing.OBJECTIVES:We have tested the therapeutic potential of iPSC-derived macrophages in a humanized disease model of hereditary pulmonary alveolar proteinosis (PAP). Hereditary PAP is caused by a genetic defect of the GM-CSF (granulocyte-macrophage colony-stimulating factor) receptor, which leads to disturbed macrophage differentiation and protein/surfactant degradation in the lungs, subsequently resulting in severe respiratory insufficiency.METHODS:Macrophages derived from human iPSCs underwent intrapulmonary transplantation into humanized PAP mice, and engraftment, in vivo differentiation, and therapeutic efficacy of the transplanted cells were analyzed.MEASUREMENTS AND MAIN RESULTS:On intratracheal application, iPSC-derived macrophages engrafted in the lungs of humanized PAP mice. After 2 months, transplanted cells displayed the typical morphology, surface markers, functionality, and transcription profile of primary human alveolar macrophages. Alveolar proteinosis was significantly reduced as demonstrated by diminished protein content and surfactant protein D levels, decreased turbidity of the BAL fluid, and reduced surfactant deposition in the lungs of transplanted mice.CONCLUSIONS:We here demonstrate for the first time that pulmonary transplantation of human iPSC-derived macrophages leads to pulmonary engraftment, their in situ differentiation to an alveolar macrophage phenotype, and a reduction of alveolar proteinosis in a humanized PAP model. To our knowledge, this finding presents the first proof-of-concept for the therapeutic potential of human iPSC-derived cells in a pulmonary disease and may have profound implications beyond the rare disease of PAP.

Different methods of telomere length measurement are used to identify patients with telomeropathies. In our lab, we established four different methods for telomere length measurement, terminal restriction fragment (TRF) analysis by Southern blot analysis, quantitative PCR (qPCR), quantitative telomere/centromere fluorescence in situ hybridization (T/C-FISH) and fluorescence in situ hybridization combined with flow cytometry (FlowFISH). The methods each have distinct properties and apart from this-according to our experience and data-may have an impact on the individual result. In this study, we therefore compared and validated these methods measuring 154 healthy individuals of different age groups (newborn-81 years). A linear decline was found for every method (Southern blotting 64 bp per year; qPCR 31 bp per year; T/C-FISH 36 bp per year; FlowFISH 50 bp per year). With the equation of the regression line the values of each method (T/S ratio, T/C value, RTL value) can be expressed in absolute kb. All methods showed acceptable accuracy. The analysis indicated good agreement between all methods, with the best agreement between T/C-FISH and FlowFISH. Here, FlowFISH was the most precise, accurate, and reproducible method compared to the other methods. Based on our data, we emphasize the influence of expertise and experience that is required to produce robust and reliable telomere length analyses. Furthermore, we want to provide the scientific community working in diagnostics and research with data-funded advice on how to choose the appropriate method to safely discriminate between natural variability and pathological telomere shortening in individual cases.

Complex karyotypes are associated with a poor prognosis in chronic lymphocytic leukemia (CLL). Using mFISH, iFISH, and T/C-FISH, we thoroughly characterized 59 CLL patients regarding parameters known to be involved in chromosomal instability: status of the genes ATM and TP53 and telomere length. Interestingly, a deletion of the ATM locus in 11q, independent of the cytogenetic context, was associated with significantly diminished risk (p<0.05) of carrying a mutation in TP53. In patients with loss or mutation of TP53, chromosomal breakage occurred more frequently (p<0.01) in (near-) heterochromatic regions. Median telomere length in patients with complex karyotypes was significantly shorter than that of healthy controls and shorter than in all other cytogenetic cohorts. Furthermore, the median telomere length of patients carrying a TP53 mutation was significantly shorter than without mutation. We conclude that telomere shortening in combination with loss of TP53 induces increased chromosomal instability with preferential involvement of (near-) heterochromatic regions.

Heritable predisposition is an important cause of cancer in children and adolescents. Although a large number of cancer predisposition genes and their associated syndromes and malignancies have already been described, it appears likely that there are more pediatric cancer patients in whom heritable cancer predisposition syndromes have yet to be recognized. In a consensus meeting in the beginning of 2016, we convened experts in Human Genetics and Pediatric Hematology/Oncology to review the available data, to categorize the large amount of information, and to develop recommendations regarding when a cancer predisposition syndrome should be suspected in a young oncology patient. This review summarizes the current knowledge of cancer predisposition syndromes in pediatric oncology and provides essential information on clinical situations in which a childhood cancer predisposition syndrome should be suspected.

Individuals with Fanconi anemia (FA) have a high risk of developing myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), yet the secondary somatic mutations lending to these malignancies remain to be further elucidated. We employed a next-generation sequencing myeloid neoplasia gene panel to determine the mutational spectrum of FA-related MDS/AML. Ten of 16 patients showed missense, nonsense, insertion or duplication mutations in 13 genes. In contrast to findings in MDS in the general population, mutations in genes involved in RNA splicing were rarely affected. Mutations in RUNX1 and genes of the RAS pathway appeared more instrumental in the pathogenesis of FA myeloid malignancies. RUNX1 mutations were associated with more advanced disease. Interestingly, one patient with refractory anemia with ring sideroblasts harbored the SF3B1 p.K700E mutation highlighting the mutation’s causative role in MDS with ring sideroblasts even in the context of FA. On the whole, our findings implicate a different genetic architecture of FA MDS/AML from adult sporadic MDS. Notably, the genetic events resemble those described in pediatric MDS.

Typical features of dyskeratosis congenita (DC) resulting from excessive telomere shortening include bone marrow failure (BMF), mucosal fragility, and pulmonary or liver fibrosis. In more severe cases, immune deficiency and recurring infections can add to disease severity. RTEL1 deficiency has recently been described as a major genetic etiology, but the molecular basis and clinical consequences of RTEL1-associated DC are incompletely characterized. We report our observations in a cohort of six patients: five with novel biallelic RTEL1 mutations p.Trp456Cys, p.Ile425Thr, p.Cys1244ProfsX17, p.Pro884_Gln885ins53X13, and one with novel heterozygous mutation p.Val796AlafsX4. The most unifying features were hypocellular BMF in 6/6 and B-/NK-cell lymphopenia in 5/6 patients. In addition, three patients with homozygous mutations p.Trp456Cys or p.Ile425Thr also suffered from immunodeficiency, cerebellar hypoplasia, and enteropathy, consistent with Hoyeraal-Hreidarsson syndrome. Chromosomal breakage resembling a homologous recombination defect was detected in patient-derived fibroblasts but not in hematopoietic compartment. Notably, in both cellular compartments, differential expression of 1243aa and 1219/1300aa RTEL1 isoforms was observed. In fibroblasts, response to ionizing irradiation and non-homologous end joining were not impaired. Telomeric circles did not accumulate in patient-derived primary cells and lymphoblastoid cell lines, implying alternative pathomechanisms for telomeric loss. Overall, RTEL1-deficient cells exhibited a phenotype of replicative exhaustion, spontaneous apoptosis and senescence. Specifically, CD34(+) cells failed to expand in vitro, B-cell development was compromised, and T-cells did not proliferate in long-term culture. Finally, we report on the natural history and outcome of our patients. While two patients died from infections, hematopoietic stem cell transplantation (HSCT) resulted in sustained engraftment in two patients. Whether chemotherapy negatively impacts on the course and onset of other DC-related symptoms remains open at present. Early-onset lung disease occurred in one of our patients after HSCT. In conclusion, RTEL deficiency can show a heterogeneous clinical picture ranging from mild hypocellular BMF with B/NK cell lymphopenia to early-onset, very severe, and rapidly progressing cellular deficiency.

Gudrun G€ ohring*, Kathrin Thomay*, Gunnar Schmidt, Tim Ripperger, Michael Xu, Nicole Wittner, Mwe Mwe Chao, Irith Baumann, Marena Niewisch, Dirk Reinhardt, Thomas Klingebiel, Felicitas Thol, Brigitte Schlegelberger and Charlotte M. Niemeyer Institute of Human Genetics, Hannover Medical School, Hannover, Germany; Manitoba Institute of Cell Biology, CancerCare Manitoba, Winnipeg, Canada; Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany; Department of Pathology, Clinical Center, B€oblingen, Germany; Division of Pediatric Hematology and Oncology, Department of Pediatrics, University Medical Center Freiburg, Freiburg, Germany; Clinic for Pediatrics III, University Hospital Essen, Essen, Germany; Hospital for Children and Adolescents, University Hospital Frankfurt, Frankfurt, Germany; Department of Hematology, Hemostasis, Oncology and SCT, Hannover Medical School, Hannover, Germany

In pediatric acute myeloid leukemia (AML), chromosomal abnormalities leading to a disruption of the lysine methyltransferase 2A (KMT2A) gene in 11q23 are the most frequent rearrangements. Here, we report on the identification of a novel cryptic insertion, ins(11;X)(q23;q28q12), resulting in a translocation of the KMT2A gene in 11q23, leading to a KMT2A-FLNA fusion in a 13-month-old boy with de novo acute myelomonocytic leukemia, who died 38 days after diagnosis. The patient presented a complex karyotype 48∼49,Y,del(X)(q12),+del(X)(q12),+8,ins(11;X)(q23; q28q12),+19. The identified fusion gene was predicted to be out-of-frame (fusion of portions of KMT2A exon 11 with FLNA exon 11). However, RT-PCR experiments demonstrated that a potentially functional transcript was generated by alternative splicing where KMT2A exon 10 was spliced in-frame to the truncated FLNA exon 11. This case report helps to better understand the rare but potentially severe impact of KMT2A- FLNA fusions in infants with AML to improve prognostic stratification of therapy and clinical management.

Myelodysplastic syndromes (MDS) are difficult to culture long-term showing the need of a model to study the fate of cells with MDS-abnormalities associated with chromosomal instability (CIN). This approach to establish a xenograft model transplanting human hematopoietic stem cells (HSC) with different independent lentivirally-mediated MDS-related modifications into immunodeficient mice is a long-lasting and tedious experiment with many parameters and every positive as well as non-functioning intermediate step will help the research community. As the establishment of appropriate xenograft models is increasing worldwide we aim to share our experiences to contribute toward minimizing loss of mice and following the "right" approach.Here, modified HSCs were intrafemorally transplanted into NSG and/or NSGS mice: (1) RPS14-haploinsufficiency, (2) TP53-deficiency, (3) TP53 hotspot mutations (R248W, R175H, R273H, R249S). Engraftment was achieved and cytogenetic analyses showed human cells with normal karyo-types. However, in all experiments with NSG mice, mainly control cells or GFP-negative cells were engrafted, not allowing observation of modified HSCs. In NSGS mice, engraftment rate was higher, but mice developed graft-versus-host disease.In summary, engraftment of HSCs is promising and could be used to analyze the induction of CIN. However, the analysis of modified HSCs is limited and further experiments are required to improve this model.

RUNX1-associated familial leukemia is a rare hematologic malignancy. It is inherited in an autosomal dominant manner and mainly causes myelodysplastic syndrome (MDS) or acute myeloid leukemia (AML). Since constitutional mutations in RUNX1 can lead to thrombocytopenia or dysfunctional platelets, the disease is termed familial platelet disorder with associated myeloid malignancies (FPDMM, MIM 601399). Here, we report two novel families with early onset MDS illustrating the variability of the disorder.

Here we report on a child with Li–Fraumeni syndrome with a de novo TP53 mutation c.818G>A, who developed three malignancies at the age of 4 months, 4 and 5 years, respectively. We show that (i) in the choroid plexus carcinoma, the germline mutation was detected in a homozygous state due to copy‐neutral LOH/uniparental disomy, (ii) in the secondary AML, a complex karyotype led to loss of the wild‐type TP53 allele, (iii) in the Wilms tumor, the somatic mutation c.814G>A led to compound heterozygosity. The findings show that the complete inactivation of TP53 by different mechanisms is an important step towards tumorigenesis. Pediatr Blood Cancer 2015;62:1481–1484. © 2015 Wiley Periodicals, Inc.

Patients with MDS and a complex karyotype have a very short median survival and a high risk of transformation into AML. We showed earlier that TP53 mutations are associated with complex karyotype and disease progression. However, it is poorly understood how TP53 mutations contribute to the induction of chromosomal instability in hematopoietic stem and progenitor cells.