T-Lymphoblastic Lymphoma in a Patient with Pearson Syndrome Following Mitochondrial Augmentation

Pearson syndrome (PS) is an ultra-rare childhood disease caused by a deletion in the mitochondrial DNA (mtDNA). PS is associated with bone marrow dysfunction at young age, with later progression to multisystem dysfunction. A few events of myelodysplasia were reported in PS patients. Recently, mitochondrial-augmentation therapy (MAT), a process in which autologous mobilized hematopoietic CD34+ cells are infused after ex-vivo enrichment with healthy mitochondria, has been studied in patients with PS (NCT03384420 and NCT06017869).

We report on a patient diagnosed with PS at the age of 12 months, harboring a 6.7kB mtDNA deletion (m.9102-m.15815) with a 69% heteroplasmy. Her disease manifestations included anemia, thrombocytopenia, pancreatic insufficiency, hypoparathyroidism, failure to thrive and recurrent metabolic crisis events. She was treated with mitochondrial augmentation therapy at 2 years of age through a compassionate use program. Following MAT, weight gain and motor improvement were observed. Despite this, one year post MAT she had declining renal function and worsening pancytopenia. Repeated bone marrow biopsies demonstrated low cellularity per age (30-50%), with a decreased number of neutrophils and occasional small and slightly atypical megakaryocytes. Fluorescent in situ hybridization assays did not detect aberrations in chromosomes 5 or 7.

The patient was diagnosed with a mediastinal mass 26 months after MAT. A core needle biopsy was diagnostic of T-lymphoblastic lymphoma, positive for CD3, CD5, CD2, CD7, CD4, CD8, CD1a and TdT on immunohistochemistry. A polymerase-chain reaction for T-cell receptor gamma rearrangement demonstrated a monoclonal peak. An additional bone marrow biopsy confirmed low cellularity per age without evidence of leukemic involvement.

mtDNA fragments were reported to integrate into the genomic DNA, a process termed numtogenesis, occurring throughout evolution as well as in cancer. We performed long-read NGS PacBio sequencing to the tumor sample as well as pre-MAT peripheral blood DNA. The reads were mapped against the genome and the mitochondrial sequences to identify mtDNA regions inserted in the nuclear genome.

The 6.7kb mtDNA deletion was confirmed in both samples, with similar heteroplasmy of ~70%. We identified 8 areas in which mtDNA-specific sequences were integrated within the nuclear genomic DNA. All regions were identical between the tumor sample and the pre-MAT peripheral blood, four were known NUMT sites, and the longer sites were confirmed to have a different haplotype from the patients (and maternal) mitochondria. In addition, somatic mutations in T-cell malignancy associated genes were found in the tumor itself, including mutations in NRAS, FBXW7, PHF6, SUZ12, PTEN and BCOR.

The patient was treated with a combination of corticosteroids, vincristine, ARA-C, 6-mercaptopurine and methotrexate, and is currently in remission for more than 18 months.

Events of T-cell malignancies were never reported in PS patients. Despite no direct genomic integration involved in MAT, the concern of T-cell malignancies in genetically-engineered cell products initiated our investigation. We could not prove novel disruptive tumor-specific numtogenesis events. The contribution of the MAT to tumor development cannot be ruled out.