Unraveling facets of MECOM-associated syndrome: somatic genetic rescue, clonal hematopoiesis, and phenotype expansion

TO THE EDITOR:

Pathogenic germ line heterozygous variants in MECOM (myelodysplastic syndrome[MDS]1 and EVI1 complex locus) are associated with an autosomal dominant bone marrow failure (BMF) disorder characterized by radioulnar synostosis (RUS) often accompanied by amegakaryocytic thrombocytopenia (RUSAT2; Mendelian Inheritance in Man number 616738). MECOM is a transcription factor that is essential for hematopoietic stem cell self-renewal, and the loss of MECOM decreases absolute long-term hematopoietic stem cell numbers.¹ Several differentially spliced transcripts are encoded by the MECOM locus resulting in MDS1, MDS1-EVI1, and EVI1 isoforms. It has been demonstrated that these isoforms are involved in their own transcriptional regulation through distinct promoter regions and have an effect on the maintenance and transformation of hematopoietic stem and progenitor cell populations.² 

Individuals with MECOM-associated syndrome display variable clinical presentations ranging from no hematological manifestations to severe BMF with or without skeletal abnormalities.^1,3 Other features include clinodactyly, cardiac and renal malformations, hearing loss, and B-cell deficiency. Most individuals eventually progress to pancytopenia and require hematopoietic stem cell transplants at relatively young ages.^3-5 Skeletal abnormalities, particularly RUS, are seen predominantly in individuals with missense variants within the eighth and ninth zinc finger motifs of MECOM.^4,6 However, there are reports of affected individuals with premature termination variants or constitutional deletions with skeletal involvement.^7,8 

Clinical and genomics data from germ line MECOM variant carriers were collected from the Centre for Cancer Biology (Adelaide, Australia), Peter MacCallum Cancer Centre (Melbourne, Australia), Radboud University Medical Center (Radboud, The Netherlands). All procedures in this study involving human participants were performed in accordance with the Declaration of Helsinki. Studies were approved by institutional human research ethics committees and/or institutional research boards. All participants signed an informed consent form to share genomics and protected health information.

Here we report 15 cases (3 families and 5 de novo) of MECOM-associated syndrome, with onset of symptoms varying from in utero to late adulthood (Figure 1A-F). Our cohort represents the spectrum of this syndrome with individuals presenting with (1) classical RUSAT, (2) BMF (ranging from mild to severe) without RUS, and (3) RUS without hematological manifestations. Detailed information on clinical history and classification of germ line MECOM variants as per the American College of Medical Genetics guidelines are included in supplemental Information, Table 1, and supplemental Table 1.

Herein, we show that part of the variability in hematological presentation may be attributable to spontaneous reversion of germ line variants observed in some affected individuals. Our study identifies 7 of 15 affected individuals who show spontaneous resolution, alleviation of hematological symptoms, or late onset of hematological manifestation of MECOM-associated syndrome. For 4 of 6 individuals (3-II-4, 4-II-4, 5-II-1, and patient 11), amelioration of symptoms appears associated with somatic genetic rescue, in the form of copy neutral loss of heterozygosity of chromosome 3q encompassing MECOM (Figure 1H; supplemental Figures 2-4; supplemental Information), thereby duplicating the residual wild-type allele in an expanding clone. A chromosomal rearrangement involving the MECOM locus was detected by fluorescence in situ hybridization in a small subset of cells in 7-II-1. However, the consequence of this event at the cell differentiation/fitness level remains to be established. For 2 of 6 individuals, an explanation for mild presentation or symptom resolution remains enigmatic: 2-II-6 displayed spontaneous resolution of hematopoietic symptoms, whereas 4-II-1 has been free of hematological symptoms for most of her life. Longitudinal analysis of variant allele fractions in both these individuals showed no evidence of allelic imbalance (supplemental Figures 5 and 6). Somatic genetic rescue has been reported in several genetic diseases including skin disorders (eg, ichthyosis with confetti⁹ and epidermolysis bullosa¹⁰) and BMF syndromes (eg, Fanconi anemia,¹¹ Diamond Blackfan anemia,¹² Wiskott-Aldrich syndrome,¹³ and dyskeratosis congenita¹⁴), with only 1 report in MECOM-associated syndrome.¹⁵ Spontaneous normalization of blood counts and absent/mild hematopoietic involvement in carriers have been described in the literature; however, there has been limited information/follow-up as to the mechanism.^3,6,16,17 

Most reported MECOM cases have had allogeneic bone marrow transplants at relatively young ages, which could explain relatively low frequency of progression to myeloid malignancy in 5% of patients (3 adult MDS cases and 1 pediatric acute myeloid leukemia of 80 individuals¹⁸).^3,5,8 The findings of aplasia with dysplastic features in 1-II-5 and MDS in 5-II-1 adds 2 more cases of myeloid dysplasia in MECOM-associated syndrome. Notably, all 3 older individuals within our cohort (4-II-1, 4-II-4, and 5-II-1) displayed somatic variants in known age–related clonal hematopoiesis genes (supplemental Figure 7). Acquisition of somatic variants in genes such as ASXL1, DNMT3A, and TET2 have been linked with improved hematopoietic stem cell fitness and self-renewal.¹⁹ Both 3-II-4 and 4-II-4 also had transient 20q loss events (a common karyotypic abnormality observed in myeloid disorders and aging population²⁰) in their surveillance marrows. Intriguingly, 4-II-1 and 5-II-1 also have somatic ETV6 variants, which is not usually reported in an age-related context. Although the presence of such somatic alterations likely improves hematopoietic output, it may also signify an elevated risk of myeloid malignancy development, particularly with advancing age. Consistent with this, in addition to clonal haematopoiesis, 4-II-4 is beginning to exhibit dysplastic features in >1 lineage (supplemental Figure 2).

In the dynamic hematopoietic environment, demand-adapted hematopoiesis can drive mosaicism down 2 roads: clonal evolution through the acquisition of deleterious variants leading to cancer; or alternatively, revertant mosaicism resulting in partial/complete rescue of phenotype. Somatic genetic rescue is an important factor to consider in scenarios such as carriers with mild phenotype, selection of tissue sources for identification of causative lesion in individuals in remission, and use of patient-derived cell lines for drug screening. Understanding the mechanisms of revertant clonal selection in vivo and in vitro will open windows for rational correction and selection protocols for effective therapeutic intervention in inherited BMF disorders such as MECOM-associated syndrome.

Strikingly, there were 12 pregnancy losses of a total of 16 pregnancies in 5 mothers for whom detailed information regarding pregnancies was available (supplemental Table 2) within our cohort. This is a higher rate of loss (75%) than expected pregnancy outcomes in the general population (15%-25%) as well as other inherited BMF syndromes (12%-20%).^21,22 We observed recurrent pregnancy losses (including late losses) in 1-I-2, 4-II-1, and 5-II-1, all of whom are carriers of MECOM variants (Figure 1). 4-I-2, who tested negative for the MECOM variant and whose husband (4-I-1) displayed MECOM-associated phenotype, experienced stillbirth at 8.5 months of gestation (4-II-3), raising the possibility that pregnancy loss can also occur from MECOM-associated complications intrinsic to the developing fetus. Her remaining 3 children displayed symptoms of MECOM-associated syndrome with 2 testing positive for the variant, whereas the third could not be assessed due to unavailability of samples. However, we were unable to ascertain the MECOM status for the fetus. It is also worth noting that 2-I-2 and 3-I-2 (both wild-type for MECOM) have also experienced pregnancy losses. We cannot comment on whether ≥1 individuals are gonadal mosaics for the MECOM variants because we are unable to determine the MECOM status of the fetuses due to unavailability of material for genetic testing.

Cardiac and vascular abnormalities including atrial septal defect, ventricular septal defect, and patent ductus arteriosis have been reported in MECOM-associated syndrome. However, there has only been 1 report each of aortic coarcatation and aortic root dilatation.^3,23 We have observed 3 cases of aortic dilatation, with 1 progressing to an aortic aneurysm reaching the threshold for surgical correction in our cohort of 15 cases.

Overall, this report adds to the breadth of disease presentations in MECOM-associated syndrome and expands age of onset varying from in utero to late adulthood with at least 1 individual being in relatively good health well into their sixties. It is becoming increasingly clear that the complex disease presentations of MECOM-associated syndrome are primarily driven by genomic location and the nature of the germ line variants, and these presentations are further complicated by mechanisms such as somatic genetic rescue and, possibly, somatic compensation by other genes. The clinical presentation and threshold of somatic genetic rescue required for phenotypic improvement/reversion is likely dictated by how severe the impact on protein function/output is in each affected individual. The prevalence of somatic genetic rescue provides a rationale for gene-corrected autologous transplantation or direct gene editing approaches as potential treatments for the hematopoietic phenotype of MECOM-associated syndrome in the absence of matched donors. The presence of clonal hematopoiesis of indeterminate potential in the older individuals, and the finding of additional cases of myeloid dysplasia in our cohort warrant consideration of surveillance particularly in older carriers. Given the high rate of pregnancy losses in these families, they should be considered for counseling for reproductive planning and the use of preimplantation genetic diagnosis to reduce the risk of future pregnancy losses. Moreover, the variability of presentation can make accurate genetic diagnosis challenging, and the notable prevalence of somatic genetic rescue reiterates the importance of using DNA from nonhematopoietic tissue such as hair follicles or skin fibroblasts for genetic testing.

Acknowledgments: The authors thank the families and individuals for their participation in these studies.

This research was supported by funding from the National Health and Medical Research Council (NHMRC) of Australia (APP1164601), the Genomics Health Futures Mission–Medical Research Futures Fund (GHFM76777), the 2021 Early to Mid-Career Researchers-Medical Research Futures Fund (APP2023357), Maddie Riewoldt’s Vision (MRV0017 [P.V.]; MRV0023 and MRV0025), the Royal Adelaide Hospital Research Fund (P.A.), the Wilson Centre for Blood Cancer Genomics, and Melbourne Genomics Health Alliance. S.T.C is supported by an Australian NHMRC Senior Research Fellowship (APP1116974, 2018-2022) and Investigator Grant Level L3 (APP2017952, 2023-2027). A.M.B. is supported by a University of Sydney Research Training Scholarship. A.M.B and this study are supported by NHMRC Medical Research Future Funded “RNA for Rare Disease” research funding (MRF2015930, 2022-2025). Part of this study is funded by Lenity Australia, a not-for-profit philanthropic organization, and from the Sydney Children’s Hospitals Foundation, a registered charity.

Contribution: P.V. wrote the manuscript and was involved in all aspects of the project including designing the research, manuscript preparation, collecting/analyzing experimental and clinical data, and American College of Medical Genetics and Genomics variant classification; C.N.H., H.S.S., and A.L.B. were involved in research design, data analysis, manuscript preparation, and providing scientific insight; P.A., L.C.F., A. Simons, and D.K.H. were involved in different aspects of design and analysis of clinical and experimental data and manuscript preparation; M.S.B.F., A.B., S.T.C., T.T.H., K.A., S.G., K.S.K., R.K., K.H., M. Babic, A.M., L.R., C.V., L.D., R.F., and D.L. carried out different aspects of experimental design and/or data analysis; D.K.H., P.G.B., A. Swift, D.M.R., L.F.D.v.V., A.B., B.G., E.F., T.C., I.K., M.H., A.A.K., F.A.K., S.d.M., P.E., Y.B., M. Bakshi, S.M.R., N.M., M.R.J., R.P.K., P. Barbaro, P. Blombery, K.P., and N.K.P. carried out collection and analysis of clinical patient information; L.A-.M. performed bioinformatic analysis; and all authors critically reviewed and approved the manuscript.

Conflict-of-interest disclosure: S.T.C. is a volunteer member of ClinGen Expert Panels: Muscular Dystrophies and Myopathies Gene Curation Expert Panel and Limb Girdle Muscular Dystrophy Variant Curation Expert Panel; is named inventor of intellectual property (IP) relating to novel methods to identify splicing variants (PCT/AU2019/000141; PCT/AU2020/050234), which is jointly owned by The University of Sydney and The Sydney Children’s Hospitals Network; serves as the director of Frontier Genomics Pty (Sydney, Australia), which has licensed this IP; and performs this director role outside of her UniSydney position and currently receives no consultancy fees or other remuneration for it. Frontier Genomics has not traded and has no existing financial relationships that will benefit from publication of these data. The remaining authors declare no competing financial interests.

Correspondence: Hamish S. Scott, Department of Genetics and Molecular Pathology, Centre for Cancer Biology, SA Pathology, PO Box 14, Rundle Mall, Adelaide, 5000, SA, Australia; email: hamish.scott@sa.gov.au.