Type and level of RMRP functional impairment predicts phenotype in the cartilage hair hypoplasia-anauxetic dysplasia spectrum

Abstract

Mutations in the RMRP gene lead to a wide spectrum of autosomal recessive skeletal dysplasias, ranging from the milder phenotypes metaphyseal dysplasia without hypotrichosis and cartilage hair hypoplasia (CHH) to the severe anauxetic dysplasia (AD). This clinical spectrum includes different degrees of short stature, hair hypoplasia, defective erythrogenesis, and immunodeficiency. The RMRP gene encodes the untranslated RNA component of the mitochondrial RNA-processing ribonuclease, RNase MRP. We recently demonstrated that mutations may affect both messenger RNA (mRNA) and ribosomal RNA (rRNA) cleavage and thus cell-cycle regulation and protein synthesis. To investigate the genotype-phenotype correlation, we analyzed the position and the functional effect of 13 mutations in patients with variable features of the CHH-AD spectrum. Those at the end of the spectrum include a novel patient with anauxetic dysplasia who was compound heterozygous for the null mutation g.254_263delCTCAGCGCGG and the mutation g.195C-->T, which was previously described in patients with milder phenotypes. Mapping of nucleotide conservation to the two-dimensional structure of the RMRP gene revealed that disease-causing mutations either affect evolutionarily conserved nucleotides or are likely to alter secondary structure through mispairing in stem regions. In vitro testing of RNase MRP multiprotein-specific mRNA and rRNA cleavage of different mutations revealed a strong correlation between the decrease in rRNA cleavage in ribosomal assembly and the degree of bone dysplasia, whereas reduced mRNA cleavage, and thus cell-cycle impairment, predicts the presence of hair hypoplasia, immunodeficiency, and hematological abnormalities and thus increased cancer risk.

Figure 1.

Clinical and radiographic features of the novel patient with the AD phenotype. A, Female patient at age 10 years, showing severe disproportionate short stature. B and D, Radiographs of the axial and appendicular skeleton at age 8 years. The spine is abnormal, with thoracolumbar scoliosis and foreshortened vertebral bodies (on lateral film) showing anterior and posterior scalloping at the lumbar level. The end plates are slightly convex. The pelvis shows coxa vara with dysplastic femoral heads and severe shortening of the femoral necks. The femur, tibia, and fibula are short, with severe metaphyseal changes. The knee epiphyses are small and flattened. There is mesomelic shortening in the upper limbs. C, Hand radiograph taken at age 9 years. Metaphyseal changes are apparent in the wrists, with shortening of the distal ulna and ulnar kinking of the distal radius. The phalanges and metacarpals are short and broad (bullet-shaped middle phalanges), with small epiphyses already attached to the metaphyses.

Figure 2.

A, Schematic drawing of RMRP (top) and degree of RMRP evolutionary conservation (bottom), categorized into four levels by sequence alignment of nine species. The length between the TATA box and the transcription start site is conserved at 24–26 bp. This distance is known to be important for proper binding of the RNA polymerase III transcription factor complex (TFIIIB) and is altered by insertions, duplications, and triplications, leading to reduced transcription.^,, SP1 = SP1 binding site; octamer = octamer element; PSE = proximal sequence element. Nucleotides for which disease-related mutations have been published are in red; polymorphic sites are in blue. B, Mapping of evolutionary conservation of RMRP nucleotides to its two-dimensional structure. Green indicates moderately to highly conserved nucleotides. Nucleotides for which disease-related mutations have been published are boxed in red; polymorphic sites are boxed in blue. Red arrows indicate insertion or deletion mutations; blue arrows indicate insertion or deletion polymorphisms. Note that disease-related mutations, which do not affect conserved nucleotides, lead to mispairing in stem structures.

Figure 3.

Correlation of phenotype scores for mutations analyzed, with reference to degree of bone dysplasia, hair hypoplasia, and immunodeficiency/hematological abnormalities. A, Results of 5.8S rRNA cleavage activity normalized to wild-type activity as a function of ribosomal assembly in 13 mutations, compared with the respective skeletal phenotype score, revealing a significant negative correlation between degree of bone dysplasia and rRNA cleavage activity (R=-0.8346; P=.0008). rRNA cleavage was most affected by the AD mutations g.111_112insACGTAGACATTCCT and g.90_91AG→GC. An intermediate effect was observed for the AD mutation g.254C→G; mutation g.195C→T, identified in the new patient with AD as well as in patients with CHH and MDWH; and mutations g.126C→T, g.220T→C, g.261C→T, g.4C→T, g.63C→T, and g.96_97dupTG, leading to the milder phenotypes. The least effect was seen for g.146G→A, g.248C→T, and g.70A→G. Red columns represent AD mutations, yellow columns represent CHH and MDWH mutations, and orange columns represent AD, CHH, and MDWH mutations. B, Results of mRNA cleavage activity normalized to wild-type activity as a function of cell-cycle progression in 13 mutations, compared with the respective immunological/hematological phenotype score and the incidence of hair hypoplasia. Notably, the presence of impaired mRNA cleavage activity strongly correlates with the immunological/hematological phenotype and the likelihood of hair hypoplasia (R=-0.8429 [P=.0007] and R=-0.8115 [P=.001], respectively).

Figure 4.

Two-dimensional structure of the RNase MRP complex. The RMRP gene encodes the untranslated RNA component of the mitochondrial RNA–processing ribonuclease. Nucleotides mutated in milder phenotypes are shaded yellow, those mutated in the severe skeletal phenotype are shaded red, and the mutation observed in both milder and severe skeletal phenotypes is shaded orange. Recently, it was shown that the proteins Rpp20, Rpp21, Rpp25, Rpp30, Rpp38, hPop1, and hPop4 interact directly with the RNA frame formed by the RMRP transcript, whereas hPop5 and Rpp14 do not.^,, Our results also indicate a predominant participation of the P1, P2, and P19 domains, as well as the P8, P9, and P12 domains, in the rRNA cleavage function, whereas parts of the P3 and P4 domains seem to be involved mainly in mRNA cleavage.