Copy neutral loss of heterozygosity: a novel chromosomal lesion in myeloid malignancies

Abstract

Single nucleotide polymorphism arrays (SNP-A) have recently been widely applied as a powerful karyotyping tool in numerous translational cancer studies. SNP-A complements traditional metaphase cytogenetics with the unique ability to delineate a previously hidden chromosomal defect, copy neutral loss of heterozygosity (CN-LOH). Emerging data demonstrate that selected hematologic malignancies exhibit abundant CN-LOH, often in the setting of a normal metaphase karyotype and no previously identified clonal marker. In this review, we explore emerging biologic and clinical features of CN-LOH relevant to hematologic malignancies. In myeloid malignancies, CN-LOH has been associated with the duplication of oncogenic mutations with concomitant loss of the normal allele. Examples include JAK2, MPL, c-KIT, and FLT3. More recent investigations have focused on evaluation of candidate genes contained in common CN-LOH and deletion regions and have led to the discovery of tumor suppressor genes, including c-CBL and family members, as well as TET2. Investigations into the underlying mechanisms generating CN-LOH have great promise for elucidating general cancer mechanisms. We anticipate that further detailed characterization of CN-LOH lesions will probably facilitate our discovery of a more complete set of pathogenic molecular lesions, disease and prognosis markers, and better understanding of the initiation and progression of hematologic malignancies.

Figure 1

Classification of CN-LOH. CN-LOH can be classified by either its origin or its location. CN-LOH can have an acquired, clonal derivation or a constitutional, nonclonal derivation. Nonclonal CN-LOH can be the result of an early embryonic mitotic event, leading to mosaicism, or may be truly constitutional. This constitutional CN-LOH can arise from autozygosity or meiotic events, including trisomic rescue, gamete complementation, duplication of a monosomic chromosome in an aneuploid zygote, or nonhomologous recombination. In addition, CN-LOH can be either segmental or numerical. Segmental CN-LOH arising from one crossing over will be telomeric (a, bottom left), whereas 2 crossing-over events will lead to interstitial CN-LOH (b). CN-LOH can also involve an entire chromosome (numeric; c, d, and e).

Figure 2

Mitotic mechanisms of formation of CN-LOH. (A) CN-LOH can occur as the result of mitotic recombination between homologous chromosomes. Depending on how the chromosomes are sorted during mitosis, daughter cells with CN-LOH can arise. (B) CN-LOH can also arise as the consequence of deletion followed by recombination using the homolog as a template for correction.

Figure 3

Determination of acquired versus germline nature of CN-LOH. Acquired CN-LOH (red bar, top left) is identified when allelic imbalance (as shown by genotyping calls) with normal copy number (top track) in bone marrow and not CD3⁺ cells (representing the germline configuration). Top left: An example of acquired CN-LOH of chromosome 7. A region of homozygosity and diploid copy number (as indicated by the red bar) are seen in bone marrow only. Top right: An example of germline CN-LOH of chromosome 20. Runs of homozygosity (red bars) are present in both bone marrow and CD3⁺ cells. Among a cohort of 1003 healthy controls, CN-LOH was mainly interstitial (bottom left) and ranged in size from 0.3 to 65 Mb (median, 8.7 Mb; bottom center). Bottom right: The distribution of nonclonal, germline CN-LOH in controls on an exemplary chromosome (chromosome 6).

Figure 4

Genomic distribution of acquired CN-LOH in MDS/secondary AML and primary AML. CN-LOH is nonrandomly distributed across the genome in both MDS/secondary AML (blue lines) and primary AML (red lines), with some chromosomes and chromosomal regions being more frequently affected.

Figure 5

Pathogenic actions of LOH, both CN-LOH and deletion. CN-LOH can lead to the duplication of a disease-linked minor germline variant (top line, left) or an acquired mutation (top line, right). It can also lead to increased gene expression by the loss of a negative epigenetic mark (second line, left) or decreased gene expression by the duplication of a repressive epigenetic mark (second line, right). Deletion of chromosomal material can lead to the unveiling of a minor germline variant (third line, left) of acquired mutation (third line, right), resulting in hemizygosity. Furthermore, deletion can affect gene expression: it can lead to increased expression through loss of an imprinted allele, repression by loss of the expressed allele, or haploinsufficiency.