Karyotypic and Genetic Abnormalities Associated with Clonal Evolution in Paroxysmal Nocturnal Hemoglobinuria.
Authors: Makishima Hideki , Yoshida Kenichi , Clemente Michael J. , Sanada Masashi , Nagata Yasunobu , Afable Manuel G. , Jerez Andres , Chiba Kenichi , Shiraishi Yuichi , Miyano Satoru , Ogawa Seishi , Maciejewski Jaroslaw P. 
Published: October 2019

Abstract
Abstract 2371
PNH is a clonal stem cell disease. While nonmalignant, PNH shows certain similarities to MDS and other neoplasms affecting hematopoietic stem and progenitor cells, including persistence of an aberrant clone, clonal expansion, and phenotypic abnormalities. In a small proportion of patients, subtle chromosomal abnormalities can be found and cases of otherwise classical PNH due to microdeletions involving the PIG-A locus have been described, illustrating similarities to other malignant conditions. PIG-A gene mutations lead to defective biosynthesis of GPI anchors and are responsible for the PNH phenotype. Similarly, phenotypic features of stem cells affected by PIG-A mutations are believed to be responsible for the extrinsic growth advantage and clonal expansion in the context of immune mediated suppression of hematopoiesis. While this scenario is plausible, there are also observations suggesting that intrinsic factors may be also involved. For instance, PNH persists after successful immunosuppression, often for many years, suggesting activation of stem cell maintenance genes. Furthermore, PNH clones can also be encountered (albeit at a very low frequency) in healthy individuals, and PNH can present in a pure form without aplastic anemia. Such extrinsic factors may include additional, secondary genetic events such as somatic mutations. Supporting this theory, clonal rearrangement of chromosome 12, which leads to overexpression of the transcription factor HMGA2 gene, were found in cells with the PIG-A mutation from 2 PNH cases. Also, we recently reported 3 PNH cases with JAK2 V617F mutation, who presented with a MPN phenotype and thrombosis.
We theorized that study of clonal architecture in PNH will reveal clues as to the pathogenesis of clonal evolution of the PNH stem cell. We applied next generation whole exome sequencing to detect somatic mutations in PNH cases (N=6). The subsequent validation set included 45 PNH cases. PNH and non-PNH cells were sorted using magnetic beads. DNA from both fractions was analyzed by whole exome sequencing and results of the non-PNH cells were subtracted from the results of the PNH clone. We found biallelic PIG-A mutations in 2 female cases and a single mutation in each male case. In an index female case with thrombosis, a novel somatic heterozygous mutation of NTNG1 (P24S) was detected, while the patient was negative for the JAK2 mutation. Allelic frequency with the NTNG1 mutation (53/160 sequence reads (33%)) was larger than that with a concomitant heterozygous PIG-A mutation (intron 5 splice donor site G<A) (78/333 reads (23%)). In this case, the size of the other heterozygous PIG-A mutation (G68E) was less (31/194 (16%)) than the other PNH clone. These findings suggest that there are 2 different PNH clones in one case and that the NTNG1 mutation might be acquired before PIG-A gene was mutated. Moreover, NTNG1 encodes a GPI-anchored cell membrane protein and the mutation (P24S) was located in the predicted signal peptide. All together, 3 novel mutations were discovered, including MAGEC1 (C747Y) and BRPF1 (N797S) mutations. Of note, BRPF1 mutations have been also reported in AML. Interestingly, BRPF1 encodes a component of MOZ/MORF complex, positively regulating the transcription of RUNX1.
To screen pathogenic karyotypic lesions in PNH clonal expansions, we combined metaphase cytogenetics and single nucleotide polymorphism arrays. We detected 14 somatic chromosomal abnormalities in 13 out of 26 PNH cases (50%). Of note is that a microdeletion on 2q13 resulted in the loss of an apoptosis-inducing gene BCL2L11, suggesting a contribution to growth advantage. Somatic UPD lesions strongly suggest the presence of homozygous mutations, for example the SET nuclear oncogene, which is located in UPD9q32qter was observed in another PNH case. Overall, the discovery of these novel mutations, as well the previously described JAK2 mutation, indicates that the pathophysiology of PNH clonal evolution partially overlaps that of other myeloid malignancies.
In sum, various novel somatic karyotypic abnormalities and mutations are frequently detected in PNH clones using technology with comprehensive and high resolution. Some of these aberrations play a similar role in the clonal evolution of myeloid malignancies. These results suggest new therapeutic strategies similar to those for other myeloid malignancies should be considered in PNH cases with addition mutations.

Disclosures:
Makishima: Scott Hamilton CARES Initiative: Research Funding. Maciejewski:NIH: Research Funding; Aplastic Anemia&MDS International Foundation: Research Funding.