Screening for clonal hematopoiesis in patients with β-hemoglobinopathies who are candidates to transplant approaches Free

Background. Allogeneic hematopoietic cell transplantation (alloHCT) represents a currently available curative option for patients with β-hemoglobinopathies, including Sickle Cell Disease (SCD) and Transfusion-Dependent Thalassemia (TDT). Recent evidence indicates that clonal hematopoiesis (CH) may increase the risk of post-transplant myeloid malignancies; in particular, TP53 mutations detected before transplantation have been linked to the development of such malignancies in SCD patients who experienced graft rejection. Gene therapy (GT) also holds promise as a curative approach for β-hemoglobinopathies, although long-term follow-up data are still limited. Reported cases of acute leukemia following GT in SCD patients suggest that the use of high-dose alkylating agents in conditioning regimens may contribute to the development of secondary malignancies. CH is increasingly recognized in SCD patients at younger ages than in the general population, potentially due to chronic inflammation, erythropoietic stress, and prior exposure to cytotoxic therapies. These findings underscore the need for systematic pre-transplant CH molecular screening to allocate patients in one or other of the curative transplant options and reinforce the post-transplant surveillance in case of detected CH.

Methods. We conducted a prospective screening for CH in peripheral blood from SCD and TDT patients who are candidates to alloHCT or GT between 2020 and 2025. A targeted high-throughput capture panel covering 43 genes involved in CH or myeloid malignancies (Agilent SureSelect CD HMH Myeloid Cancer Panel) and sequenced on MiSeq (Illumina) was used to identify rare hematopoietic cells carrying somatic mutations (validated LOD = 0.3% on hotspots and 0.4% on all covered regions). All variants with an allelic frequency (VAF) above the LOD and below 40% were considered clonal. Those with a VAF between 40-60% were retained when classified as pathogenic or possibly pathogenic according to clinical standards or filtered as variants of unknown significance otherwise.

Results. Sixty patients were included in the analysis (56 SCD and 4 TDT). Among them, 20% (12/60; 11 SCD and 1 TDT) had CH with a median variant allele frequency (VAF) of 1.2% [0.7-3.5] (min-max), and up to five mutations per patient. One patient carried a confirmed germline TP53^c.783-1G>A (NM_000546.5) mutation in the context of a Li-Fraumeni syndrome. Among patients with CH detected, the most frequently mutated genes were DNMT3A (29%), TP53 (29%), PPM1D (29%), and ASXL1 (21%). The median age of patients with CH was 39.5 years, [35–46] (95%CI) compared to 35 years [28–42] for others (p=0.04, Student t-test with Welch correction).

Non-Myeoabltive-AlloHCT were performed in 24 SCD patients, including 23 geno-identical (GI) and one haplo-identical transplant. Two GI-allograft patients carried somatic mutations before AlloHCT so far: one with DNMT3A^Phe732del (1.0%) and DDX41 ^Lys9* (1.3%) mutations who had low donor T-cell chimerism levels at last follow up after 4 months post-AlloHCT (donor CD3+ at 5%); and another with a CUX1^Asp801Asn (1.3%) mutation with no signs of rejection at 13 months of follow up (donor CD3+ at 36%). One SCD patient experienced a graft rejection at 5 months of follow-up (donor CD3+ at 0%) with no HC detected before GI-allograft.

GT with CRISPR-Cas9–based gene editing approach was performed in a 35 years old TDT patient carrying a mutation DNMT3A^Cys562Gly (VAF=1.5%) pre-GT; similar rates of detection (1.1%) was observed at 4 months of last follow-up. GT with Lentiviral vector-based approach was performed in a 35 years old SCD patient carrying a PPM1D^p.Ser543fs mutation (VAF=0.7 %) pre-GT with no detection of mutation at 54 months of follow up. Additionally, one patient acquired a DNMT3A^Leu637Gln (2.6%) clone, detected 34 months post-AlloHCT, which was retrospectively identified in his/her sibling donor (VAF pre-transplant=1%). No secondary malignancy was observed during follow-up.

Conclusion. Our findings confirm that a significant proportion of SCD patients harbor CH before alloHCT. The presence of high-risk mutations, such as those in TP53, supports the integration of molecular profiling into pre-transplant evaluation. Future prospective studies are warranted to evaluate the prognostic impact of specific mutations and to refine clinical guidelines for CH surveillance following transplant curative approaches.