Diminutive somatic deletions in the 5q region lead to a phenotype atypical of classical 5q- syndrome

Abstract

Classical 5q- syndrome is an acquired macrocytic anemia of the elderly. Similar to Diamond Blackfan anemia (DBA), an inherited red cell aplasia, the bone marrow is characterized by a paucity of erythroid precursors. RPS14 deletions in combination with other deletions in the region have been implicated as causative of the 5q- syndrome phenotype. We asked whether smaller, less easily detectable deletions could account for a syndrome with a modified phenotype. We employed single-nucleotide polymorphism array genotyping to identify small deletions in patients diagnosed with DBA and other anemias lacking molecular diagnoses. Diminutive mosaic deletions involving RPS14 were identified in a 5-year-old patient with nonclassical DBA and in a 17-year-old patient with myelodysplastic syndrome. Patients with nonclassical DBA and other hypoproliferative anemias may have somatically acquired 5q deletions with RPS14 haploinsufficiency not identified by fluorescence in situ hybridization or cytogenetic testing, thus refining the spectrum of disorders with 5q- deletions.

Figures

Figure 1

SNP array genotyping demonstrates mosaic deletions of chromosome 5q that overlap the 5q33 CDR in 2 patients. Regions of copy loss (shaded) are indicated by decreased log R signal ratio (LRR). Splitting of the heterozygous minor allele frequencies (MAFs) around the expected 0.5 level in regions of reduced copy number indicates mosaic monosomy/disomy (arrows). The displayed region of chromosome 5q is boxed in the ideogram. (A) Patient 1 has 2 apparently discrete regions of mosaic monosomy in 64% of peripheral blood DNA: a 16.1-Mb deletion extending from chr5:141 108 260 to 157 224 755 (involving PCDH1 to CLINT1) that includes all of the 5q33 CDR, as well as a more centromeric, 1.5-Mb deletion at chr5:110 887 600 to 112 390 739 (involving STARD4 to MCC). Similarities in LRR and MAF signal values at both regions in this and subsequent experiments (Figure 2) suggest the possibility of an intrachromosomal rearrangement joining the 2 regions. (B) Analysis of patient 1 mosaicism indicates a nonuniform distribution of copy loss in circulating cell fractions and improvement with lenalidomide treatment. Mosaicism was estimated to involve 64% of whole-blood DNA at the larger deletion region. Lymphoid-enriched (CD3+ or CD19+) and myeloid-enriched (CD3− and CD19−) DNA prepared from magnetic bead-separated peripheral blood populations showed substantial disparity, with monosomy estimated in only 27% of the lymphoid but 82% of the myeloid population. Similar analysis of the myeloid fraction from blood obtained after 3 months of treatment with lenalidomide showed marked diminution of the monosomic fraction to an estimated 31% of myeloid DNA. Similar changes were also observed in the smaller deletion region (not shown). (C) Patient 2 has an 897-Kb deletion extending from chr5:149 496 080 to 150 393 600 (involving PDGFRB to TNIP1), with monosomy in 77% of the peripheral blood DNA sample. This deletion is approximately half the size and is entirely contained within the current 5q33 CDR. The 5q33 CDR and genes with potential relevance to the 5q syndrome are indicated above the chromosome. Coordinates are expressed relative to National Center for Biotechnology Information Build 36.1.

Figure 2

Lenalidomide treatment normalizes bone marrow mRNA expression and colony-forming potential. (A) Bone marrow expression of RPS14 as measured by quantitative real-time PCR is markedly increased with lenalidomide treatment and the concomitant reductions in 5q mosaic monosomy. Gene set enrichment analysis comparing pre- and post-lenalidomide-treatment bone marrow mRNA expression demonstrates significant increases in (B) erythroid differentiation program (False Discovery Rate < 0.05) and (C) a decrease in expression of p53 target genes, a putative mediator of ribosomal protein haploinsufficiency. (D) The in vitro colony-forming potential for BFU-E, CFU-E, and to a lesser extent, CFU-GM was also significantly improved with lenalidomide therapy. *P value of Student t test < .05; **P value of student t test < .005; ***P value of student t test < .001; error bars denote SEM.