Ring Chromosomes in Hematological Malignancies Are Associated with TP53 Gene Mutations and Characteristic Copy Number Variants

Abstract

Ring chromosomes (RC) are present in <10% of patients with hematological malignancies and are associated with poor prognosis. Until now, only small cohorts of patients with hematological neoplasms and concomitant RCs have been cytogenetically characterized. Here, we performed a conventional chromosome analysis on metaphase spreads from >13,000 patients diagnosed with hematological malignancies at the Johns Hopkins University Hospital and identified 98 patients with RCs-90 with myeloid malignancies and 8 with lymphoid malignancies. We also performed a targeted Next-Generation Sequencing (NGS) assay, using a panel of 642 cancer genes, to identify whether these patients harbor relevant pathogenic variants. Cytogenetic analyses revealed that RCs and marker chromosomes of unknown origin are concurrently present in most patients by karyotyping, and 93% of patients with NGS data have complex karyotypes. A total of 72% of these individuals have pathogenic mutations in TP53, most of whom also possess cytogenetic abnormalities resulting in the loss of 17p, including the loss of TP53. All patients with a detected RC and without complex karyotypes also lack TP53 mutations but have pathogenic mutations in TET2. Further, 70% of RCs that map to a known chromosome are detected in individuals without TP53 mutations. Our data suggest that RCs in hematological malignancies may arise through different mechanisms, but ultimately promote widespread chromosomal instability.

Keywords: complex karyotype; copy number variants; gene mutation; myeloid malignancies; ring chromosomes.

Figure 1

Chromosomal abnormalities in RC patients with myeloid-derived cancers. (A) Distribution of the frequency with specific chromosomal abnormalities is seen among 90 karyotypes from patients with myeloid-derived cancers and RC (dmin = double-minute chromosome; − = chromosomal deletion; + = chromosomal addition; add = addition of unknown origin; del = segmental deletion; der = derivative chromosome; dic = dicentric chromosome; dup = segmental duplication; i = isochromosome; idic = isodicentric chromosome; ins = insertion; inv = inversion; r (chr) = chromosome-derived RC; t = translocation). (B) Distribution of the number of myeloid-derived cancer patient karyotypes with at least one structural abnormality for a given chromosome. (C) The frequency of segmental deletions. (D) unknown additions seen in the p arms and q arms of affected chromosomes, across 90 karyotypes from patients with myeloid-derived cancers.

Figure 2

(A) Oncoplot of patients with myeloid-derived malignancies and RCs, including the (B) distribution of mutation type among each affected gene. Patient # was from the Table S1.

Figure 3

Gene mutations in RC patients with myeloid-derived cancers. (A) Distribution of the frequency of specific chromosomal abnormalities seen among 39 karyotypes from patients with myeloid-derived cancers that possess pathogenic variants in TP53. (B) Distribution of the frequency of specific chromosomal abnormalities seen among eight karyotypes from patients with myeloid-derived cancers that possess pathogenic variants in TET2. (C) Distribution of the frequency of specific chromosomal abnormalities seen among seven karyotypes from patients with myeloid-derived cancers that possess pathogenic variants in NRAS. (D) Distribution of the frequency of specific chromosomal abnormalities seen among 19 karyotypes from patients with myeloid-derived cancers that do not possess pathogenic variants in TP53 (dmin = double-minute chromosomes; − = chromosomal deletion; + = chromosomal addition; add = addition of unknown origin; del = segmental deletion; der = derivative chromosome; dic = dicentric chromosome; dup = segmental duplication; i = isochromosome; idic = isodicentric chromosome; ins = insertion; inv = inversion; r (chr) = chromosomal-derived ring chromosome; t = translocation).

Figure 4

TP53 mutations and chromosomal abnormalities in myeloid RCs. (A) Chromosome 17 ideogram indicating the cytogenetic position of TP53 and various structural abnormalities (add = unknown addition; der = derivative chromosome; dic = dicentric chromosome; i = isochromosome; idic = isodicentric chromosome). (B) TP53 protein structure with the relative locations of amino acid changes associated with TP53 mutations (Mut = TP53 mutation; Mut 1/1 = the only TP53 mutation in that patient; Mut 1/2 = one of the two mutations in a patient; * = nonsense; del = deletion; fs = frameshift; NLS = nuclear localization signal).

Figure 5

Structural rearrangements seen in karyotypes from myeloid RCs with TP53 mutations. (A) Monosomy 17 and a TP53 mutation in case 88; (B) An add(17p) and a TP53 mutation in case 38; (C) An add(17p) and TP53 mutation in case 36; (D) A derivative chromosome of 5 and 17 and a TP53 mutation in case 26; (E) A derivative chromosome of 15 and 17 and a TP53 mutation in case 90; * = nonsense mutation; (F) A dicentric chromosome of 5 and 17 and a TP53 mutation in case 24; (G) An isochromosome 17q and a TP53 mutation in case 76. Red arrows point to abnormal chromosomes, resulting in a loss of 17p, including TP53.

Figure 6

TP53 FISH in RC patients with add(17) where red = TP53 and green = centromere 17 (Cen17). (A) Normal copy number of TP53 (2R2G) with add(17q) (case 46). (B) Loss of TP53 (1R2G, red arrow points to TP53 signal) (case 27). (C) Abnormal TP53 copy number (2Rdim1R2G with red arrows pointing to two diminished fluorescence intensity signals of TP53) (case 38). (D) Loss of TP53 due to monosomy 17 (1R1G) (case 41). Cells were stained with 4′,6-diamidino-2-phenylindole (DAPI) in blue color.