Isolated isochromosomes i(X)(p10) and idic(X)(q13) are associated with myeloid malignancies and dysplastic features
Authors: Dominique Penther, Pascaline Etancelin, Daniel Lusina, Audrey Bidet, Benoit Quilichini, Baptiste Gaillard, Isabelle Rafdord‐Weiss, Marie Joelle Mozziconacci, Antoine Ittel, Catherine Roche‐Lestienne, Carole Barin, Gwendoline Soler, Agnes Daudignon, Nathalie Nadal, Elise Chapiro, Christine Lefebvre, Catherine Godon, Gwenael Nadeau, Francine Mugneret, Steven Richebourg, Pierre‐Julien Viailly, Yann Ferret, Florence Nguyen‐Khac, Virginie Eclache
Journal: American Journal of Hematology (2019)

An isodicentric X chromosome, with a breakpoint in Xq13 named idic(X)(q13), is a rare but recurrent abnormality found in about 1% of myelodysplastic syndromes (MDS), especially in old females. Most cases with idic(X)(q13) are MDS, but a number of acute myeloid leukemias (AML), usually secondary to MDS, have also been reported, and a few cases of myeloproliferative neoplasms (MPN).1 The idic(X)(q13) is frequently the only cytogenetic abnormality, albeit one or more copies of the idic, beside a normal X chromosome being present in the same cells. This suggests that idic(X)(q13) may be implicated in the early process of the disease. The presence of idic(X)(q13) is specifically associated with MDS in the WHO classification. Its clonal detection by conventional cytogenetics is sufficient to diagnose MDS, in case of cytopenias without morphological dysplasia.2 Conversely, the isochromosome of the short arm of chromosome X named i(X)(p10) is a very rare abnormality. It is observed in some cases of myeloid or lymphoid malignancies, both as a unique abnormality, and as part of a more complex karyotype, in female, and less frequently in male patients. Myelodysplastic syndromes evolution is heterogeneous with transformation to AML in about 30% of cases. An International Prognostic Scoring System (IPSS) is commonly used to predict leukemic evolution of primary untreated adults and to adapt therapy. Revised (R) in 2012,3 this score includes bone marrow blast percentage, hemoglobin level, absolute neutrophil count, platelet count and cytogenetics. There is no definite prognostic impact from Idic(X)(q13), and is considered as another abnormality in the intermediate group of the IPSS-R. Recently, exome and genome-wide sequencing of MDS cases revealed a great diversity of genomic aberrations, with more than 25 recurrent mutations.4 Several genes involved in pre-messenger RNA splicing have been shown to be mutated in half of MDS patients, revealing a new leukemic pathway involving spliceosome dysfunction. To characterize the clinical and genetic profile of myeloid neoplasms associated with idic(X)(q13) and i(X)(p10), we performed a retrospective study, between 2002 and 2017, of 45 patients with myeloid neoplasm who presented these abnormalities. All patients gave their informed consent in agreement with the Helsinki declaration; and the Institutional Ethics Committee at Avicenne Hospital approved this study. The Idic(X)(q13) chromosome was found in 33 cases, and the i(X)(p10) in 12 patients who were all female. Ten cases were associated with other chromosomal abnormalities mainly involving chromosomes five and seven. The analysis was then restricted to 35 patients with an isolated X chromosome abnormality. In the majority of cases (n = 29), the X chromosome abnormality was detected at diagnosis. Isochromosomes could result from transverse, instead of longitudinal misdivision of the centromere; another mechanism could be chromatid exchange involving two homologous chromosomes. In both scenarios, it leads to the loss of the long arm and gain of the short arm of chromosome X, resulting in a state of genetic imbalance. It is possible that the frequency of i(X)(p10) was previously underestimated in the literature. The cytogenetic distinction between del(Xq) and i(Xp) is difficult due to the similarity of Xp- and q-arm banding patterns, extending from the centromere to band Xq24 (Figure 1). A morphological centralized review of the bone marrow smear was performed by two cytologists. The revised diagnosis was MDS (n = 25) [MDS with ring sideroblasts (n = 1), MDS with uni (n = 1) or multilineage dysplasia (n = 10) and with ring sideroblasts (n = 2), MDS with excess blasts −1 (n = 6), MDS with excess blasts 2 (n = 3), MDS with myelofibrosis (n = 2)] or AML with multilineage dysplasia (n = 2), chronic myelomonocytic leukemia (n = 4), atypical chronic leukemia (n = 1) or unclassifiable cytopenia (n = 3). The majority of patients presented marked dysplastic features (>10%) in one or more of the major lineages. No specific feature was observed. Some patients had a history of previous neoplasia or myeloid neoplasm, including four solid tumors (breast cancer n = 3), two AML with normal karyotype and NPM1 mutation, one acute lymphoblastic leukemia, one lymphoma, one chronic myelocytic leukemia on complete remission, two immune thrombocytopenias and two monoclonal gammopathies. Nineteen analyzed patients presented a median of 2.9 mutations in the 27 genes analyzed by Next Generation Sequencing. The most frequently mutated genes were TET2 (74%), SRSF2 (68%) and ASXL1 (47%). Half of patients presented two or more mutations of TET2 (often a frameshift insertion / deletion and a stop codon). Twelve patients presented a hotspot mutation of SRSF2 (p.P95R/L/H) and one out of nine patients had the hotspot c.1934dupG mutation of ASXL1. Among the other mutated genes, we noted mutations of DNMT3A (10.5%), NRAS (10.5%), SF3B1 (10.5%), IDH1 (10.5%) and JAK2 (10.5%). Only one case had a mutation of CSF3R, CBL, IDH2, EZH2, U2AF1, RUNX1 and WT1 respectively. Interestingly, no patient presented a mutation of TP53. In 94% of cases, TET2 mutations co-occurred with other mutations, especially involving SRSF2 or ASXL1 in 11 (57.8%) and 6 cases (31.5%) respectively. Among patients with MDS, we note a frequent association between one or more TET2 mutations and a mutation of SRSF2 (Table S1). We compared the molecular profile of the i(X)(p10) group (n = 7) with the idic(X)(q13) group (n = 12). The TET2 mutations were associated with i(X)(p10) in 43% of cases, and co-occurred with the SRSF2 mutation in 66% of cases. The TET2 mutations were associated with idic(X)(q13) in 91.6% of cases, and co-occurred with SRSF2 mutation in 75% of cases. There was no significant difference between the two subgroups probably due to the small sample size. With a median follow-up of 21 months (2-114 months), 15 patients died and 8 were lost to follow-up. Nine patients with MDS evolved to a higher grade MDS or AML. Among these patients, two received stem cell transplantation and one obtained a complete remission. The other patients received various treatments such as 5-azacytidine (n = 3), a cytarabine based regimen (n = 3) or palliative care (n = 3). They were all deceased at the end of our study. In this series, the iso/isodic chromosome X was the sole abnormality in 35 cases, which suggests a role of these abnormalities in the pathologic process. No gene involved in the myelodysplastic or leukemic process was discovered in the genetic region located in Xq13.5 The mitochondrial iron transporter gene, and ATP-binding cassette transporter (ABCB7), mapped in Xq21, which is implicated in X-linked sideroblastic anemia and spinocerebellar ataxia is lost. Functional ABCB7 protein is required for mitochondrial iron homeostasis and is involved in the transport of iron from mitochondria to the cytosol.5 The ABCB7 mRNA transcript is down-regulated in case of SF3B1 mutations, resulting in an abnormal degradation of this mRNA. In our cohort, only six patients presented an excess of ring sideroblasts and SF3B1 mutations were found in two of these six patients. This observation supports that other mechanisms are implicated in the myelodysplastic features. The TET2 mutations, found in 74% of our cases, were the most frequent mutations. Two or more TET2 mutations were found in half of our patients. Previously, Paulsson et al.5 identified that 4 patients out of 11 with idic(X)(q13) carried this mutation. The TET2 mutations are usually associated with an increase in hematopoietic self-renewal due to modification of DNA methylation. They are frequent in MDS, involving approximately 20% to 30% of patients. The biallelic inactivation of TET2 seems to be an early oncogenic event.4 Two or three mutations of TET2 were observed in 9 patients out of 18, suggesting the presence of a biallelic inactivation. In patients who presented TET2, SRSF2, or ASXL1 mutations, the variant allelic frequency (VAF) of SRSF2 (m = 41%) and ASXL1 (m = 25%) were lower than TET2 VAF (m = 51%), suggesting that TET2 mutation was the first oncogenic event. Note, SRSF2 is a member of the serine/arginine-rich class of splicing factors that is involved in DNA stability. Mutations in this gene occur in 3% to 11% of early-stage MDS, and are more frequent in CMML (about 25%). Also, ASXL1 is a histone-modifying enzyme component of the polycomb repressive complex two, that regulates the stem cell differentiation and gene transcription repression. In the literature, ASXL1 mutations occurred in about 11% to 21% of MDS patients, and 10% to 15% of MPN patients, and are associated with poor prognosis.6 In our cohort of patients, the majority of cases presented mutations associated with myelodysplastic features with a median of 2.9 mutations/patient. There were no differences between the two subgroups of iso and idic patients. These results demonstrate that i(X)(p10) is a specific myeloid abnormality such as idic(X)(q13). The high level of TET2, SRSF2 and ASXL1 mutations in patients with X chromosome abnormalities, is higher than that usually found in myeloid disorders (75% vs 20% to 30% for TET2; 68% vs 15% for SRSF2; 47% vs 11% to 21% for ASXL1).4 The SRSF2 and ASXL1 mutations are usually associated with worse prognosis in MDS patients,6 contrasting with the intermediate risk of i(X)(p10)/idic(X)(q13) in the IPSS-R score. These results could have an impact on treatment strategies in the future. The authors thank L Lebas, C Calbrix (CLCC Henri Becquerel, Rouen) for their technical assistance, and M Munger for the manuscript revision. D.P., P.E. and V.E. equally participated in the study. D.P. and V.E. designed the study, P.E. and J.V. performed molecular analyzes, D.L. and V.E. reviewed the bone marrow smear and the data. All authors contributed to collected data, revised and approved the manuscript content. 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