Cancer CGH+SNP Unmasked Multiple Noncontiguous Deletions on Chromosome 7q and Cryptic Genomic Imbalances in a CMML Patient with an Apparently Balanced t(4;12) Translocation. A Case Report and Literature Re-View A

Unmasked Multiple Noncontiguous Deletions on Chromosome 7q and Cryptic Genomic Imbalances in a CMML Patient with an Apparently Balanced t(4;12) Translocation. Case Report and Literature Re-View. Biomed Sci

Chronic myelomonocytic leukemia is a clonal hematopoietic stem cell disorder with overlapping features of myelodysplastic syndromes and myeloproliferative neoplasms. Median age at diagnosis is 70 years and, in many cases, it is diagnosed occasionally. Bone marrow karyotype is normal in two thirds of patients, with a few recurrent aberrations including -Y, -7, and +8. Here, we report the case of a patient affected by dysplastic CMML-1 subtype according to the 2017 WHO classification, showing a 46,XX,del(7) (q21q36),t(4;12)(q24;q15)[18]/46,XX [2] peculiar karyotype. To assess the real nature of these chromosomal abnormalities we performed a Cancer CGH+SNP array. On chromosome 7q, we identified three noncontiguous deletions at bands q21.11-q22.1, q22.1-q32.2 and q34-q36.1, while we did not detect any copy number neutral loss. In addition, the SNP array unveiled the unbalanced nature of t(4;12), with three cryptic genomic imbalances: two deletions on chromosome 4, at bands q13.1-q13.3 and q24, and one deletion on chromosome 12, at bands q21.33-q23.1. These three deletions are known to involve many OMIM genes, including TET2 (OMIM *612839) and NFKB1 (OMIM *16401). Chromosome 7 aberrations, detected in about 20% of CMML patients with cytogenetic abnormalities, have been recognized as an adverse prognostic factor, therefore allocating to the high cytogenetic risk category. Several tumor suppressor genes map in the chromosome 7 deleted regions, such as EZH2, SAMD9L and CUX1. Deletion of these regions can contribute to disease progression and could account for the differences in patients' prognosis due to the variability of breakpoint regions on 7q.
Next-generation sequencing (NGS) analysis confirmed this result revealing a double TET2 mutation. Therefore, we underline the role of CGH arrays in CMML diagnostic workup. These tools, together with NGS, represent a valid instrument to provide insight not only in molecular pathogenesis but also in disease progression.

Case Report
Chronic myelomonocytic leukemia (CMML) is a clonal hematopoietic stem cell disorder with overlapping features between myelodysplastic syndromes (MDS) and myeloproliferative neoplasms and an inherent leukemic risk of ~15% over 3-5 years [1,2]. The 2017 WHO classification has recommended its partitioning into three categories based on peripheral blood and bone marrow (BM) blasts percentage [2]. In addition, the previously used 1994 FAB Cooperative Leukemia Group subdivision into a "dysplastic" (MD) and a "proliferative" CMML variant has been revived. Median age at diagnosis is 70 years, with a male preponderance. In many cases the diagnosis is occasional, with a median survival of 24-36 months [3]. Over the years several studies aimed to identify clinical and biological features associated with CMML survival outcomes, leading to the development of different prognostic models for individual patients' treatment decision-making [4]. Like acute myeloid leukemia, CMML patients demonstrate ~10-15 mutations per kilobase of coding DNA regions, [5] while clonal cytogenetic abnormalities are observed in 20-30% of cases, including +8, -Y, chromosome 7 abnormalities, +21, and complex karyotypes [1]. In
Here, we describe the case of a 76-year-old patient who was admitted to our hospital because of suspected CMML and for whom an array CGH was performed to better define the genomic imbalances at submicroscopic level and identify involved genes.
In    been discovered [6,7]. While chromosome 7q cytogenetic analysis could not detect the precise intervals and the genes involved in the deletion, with array CGH we identified five genes already known to have a potential role in tumorigenesis.
In details, EZH2 is a component of the polycomb repressive complex-2 and encodes for a methyltransferase, initiating epigenetic silencing of many genes involved in different cell pathways.
CUX1 encodes for a homeobox transcription factor involving in tumorigenesis, with a possible role as a tumor suppressor gene.
SAMD9 and SAMD9L compound heterozygous deletions with high frequency in adult and childhood myeloid leukemia. In contrast with previous reports, KMT2C/MLL3, despite being an epigenetic regulator acting as a gene silencer, is not involved in our deletion. In our patient, together with a del7q, we found an apparently balanced t(4;12) translocation, which was proved to be unbalanced by array CGH. The three deletions found on chromosome 4 involve many OMIM genes, with TET2 and NFKB1 playing an important role in disease progression. Somatic TET2 mutations occur in ~60% of CMML, even if they are not specific for the disease and can also be detected as a part of age-related clonal hematopoiesis. Moreover, they have not proven to negatively impact either on overall (OS) or leukemia-free survival [8,9]. On the contrary, in the absence of clonal ASXL1 involvement, TET2 mutations were shown to favorably impact on OS [10]. Interestingly, we found the coexistent loss of EZH2 due to the 11Mb deletion at bands q34-q36.1 of chromosome 7. Indeed, its deletion is known to contribute to myeloid tumorigenesis in association with TET2 variations. The was not commonly described in association with hematological malignancies, so that its biological significance remains unclear. At the same time, we cannot exclude that some of the involved genes could play a minor role in disease onset or progression.
In conclusion, this case shows both common recurrent rearrangements and rare copy number alterations. Clarifying the role of these alterations could contribute to elucidate the mechanisms involved in CMML leukemogenic network, possibly contributing to define a more accurate prognosis. This case also underlines the importance of including different molecular cytogenetic tests in CMML diagnostic workup, so providing prognostic information and a strategy to develop personalized therapies, especially considering that NGS analysis is not always available.

Disclosure of Conflicts of Interest
All the authors declare they have no potential conflicts of interest.

Ethics Approval and Consent to Participate
This study was not conducted with research intervention. Thus, ethics committee approval was not necessary.
The patient has given her written informed consent to publish her case.

Funding
The only funds used were provided by the authors' institutions.