Genotype-Phenotype Correlations in Patients with Severe Chronic Neutropenia Harboring ELANE Mutations: A Long-Term Study of the Severe Chronic Neutropenia International Registry

Autosomal dominant ELANE mutations are identified in the largest group of severe congenital neutropenia (CN) patients (pts) (ca. 30% of all cases) and in the large majority of pts with cyclic neutropenia (CyN). The predictive value of certain mutations for leukemogenesis and response to recombinant human granulocyte colony-stimulating factor (rhG-CSF) in CN and CyN are still limited.

We analyzed data from 511 pts with different heterozygous ELANE mutations (334 CN, 177 CyN) plus 5 CyN pts with homozygous ELANE p.R220Q mutations. All pts were enrolled into the Severe Chronic Neutropenia International Registry between 1994 and 2023. Clinical status, treatment response and major events (myelodysplastic syndromes (MDS), acute myeloid leukemia (AML), stem cell transplantation, death) were reviewed annually.

The overall median follow-up was 15.7 years (in 317 pts >10 years, in 199 pts >20 years). In total, 148 different ELANE mutations were identified, including 91 missense, 16 in-frame, 34 truncating, 4 splice-site, and 3 start-loss mutations. Missense mutations were most frequent in CN pts (70.4%) and splice site mutations in intron 4 in CyN pts (46.4%). Several mutations were found exclusively in CN (i.e., all start-loss mutations, p.I120F, p.C151S/Y, p.G214V/R). The p.R220Q mutation was identified only in CyN. Truncating mutations previously considered to be specific for CN, were also detected in CyN pts.

5 CyN pts with homozygous ELANE p.R220Q mutation all belong to one consanguineous family. All pts have severe clinical course compared to heterozygous family members. The clinical symptoms in homozygous patients included frequent respiratory infections, recurrent skin abscesses, regional lymphadenitis, gingivitis and dental abscesses. None of them has developed MDS or AML to date.

53 pts (10.4%) – 49 with CN and 4 with CyN – with 35 different ELANE mutations developed MDS/AML. Of these, 27 harbored missense, 12 truncating, 5 intronic, 5 inframe, and 1 start-loss ELANE mutations. One of the CyN pts carried two mutations, p.A233P and p.V235Wfs*5, on the same allele. The median age at diagnosis of MDS/AML was significantly lower in CN pts (14.8 years), compared to CyN pts (33.2 years, p = 0.02). Mutations associated with MDS/AML transformation were p.A57V/T (2/9 cases), p.V101M (2/10 cases), p.S126L (5/39 cases), p.C151Y/S (4/8 cases), p.G214R (5/13 cases), p.C223* (3/5 cases), p.Y228* (2/3 cases), and p.S230Mfs*10 (2/2 cases). Pts with these mutations had a higher risk of MDS/AML compared to pts with other mutations (HR 10.5 (95% CI 4.6 – 23.9), p<0.0001).

Mutations associated with poor or no response to rhG-CSF (median dose ≥20 mcg/kg/d) included start-loss mutations (3/8 cases), p.A57V/T (5/9 cases), p.C151Y/S (3/8 cases), G203R (2/7 cases), and p.G214R (5/13 cases). Interestingly, despite an overlap between these mutations and the development of MDS/AML, we also observed MDS/AML in pts who required lower doses of rhG-CSF and harbored other ELANE mutations.

In 292 pts with missense mutations, we observed an association between the damaging effect of the mutation on the neutrophil elastase (NE) protein structure predicted by AlphaMissense (Cheng et al., 2019) and disease course. Predicted pathogenicity scores were significantly higher in pts who developed MDS/AML (p=0.006) and those who required higher doses of rhG-CSF (>20 mcg/kg daily) (p<0.0001). Mutations detected in CN were also significantly more pathogenic compared to those in CyN (p<0.0001). Among 20 pts with missense mutations affecting NE disulfide bonds (amino acid positions 55, 71, 151, 208), 4 developed MDS/AML.

Of the 511 pts, 47 (9.2%) were deceased at the time of analysis. Causes of death were MDS- or leukemia-related in 13 cases, transplant-related in pts with MDS/AML in 12 cases, transplant-related in pts without MDS/AML in 6 cases, primary infection in 7 cases, cardiac-related in 2 cases, other malignancies in 2 cases (renal cell carcinoma in a 62-year-old female and colorectal cancer in a 59-year-old male, both with CyN), and unclassified in 5 cases.

The results of our analysis demonstrate that MDS/AML transformation can occur in patients receiving both low-dose and high-dose rhG-CSF therapy, and emphasize the key role of genetic background but not rhG-CSF dose alone, in the risk of MDS/AML development in CN and CyN. With several exceptions, AlphaMissense tool can predict the pathogenicity of individual ELANE mutations.