AMP case report: A germline GATA2 c.121C>G (p.P41A) variant in a patient with an unusual acute promyelocytic leukemia

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Shortly after achieving remission, the patient developed mild leukopenia secondary to ATRA treatment. This mild leukopenia in combination with his likely germline GATA2 variant led him to be referred for bone marrow transplant and genetic counseling. A pedigree was obtained during the genetic counseling session (Fig. 1G). Very little information is available about the patient’s biological family because he is adopted. He is familiar with his biological mother and unaware of any familial hematological disorders. It was concluded that no additional genetic testing was required for family members, and this variant has minimal impact in making treatment decisions. No plans for bone marrow transplant had been made as of the most recent follow-up in January 2023, and his mild leukopenia is monitored.

Discussion. While this patient’s clinical presentation (leukocytosis and DIC) may appear more consistent with hypogranular APL, these manifestations may also be seen in other AMLs. In addition, the morphology and immunophenotypic profile of the leukemic blasts are not typical of hypogranular APL. Specifically, the leukemic blasts do not display the characteristic bilobed or butterfly-shaped nuclei morphologically. In addition, Auer rods were not identified. Immunophenotypically, the leukemic blasts exhibited low side scatter with expression of many myeloid lineage markers and coexpression of CD34, CD117, and HLA-DR, which is unusual for APL. Although aberrant CD2 expression has been associated with FLT3-ITD in APL,² it is not specific and is frequently seen in other AMLs.

Patteet, et al., reported a case of hypogranular APL with partial coexpression of CD2, CD34, and HLA-DR.⁶ Foley, et al., also reported that the presence of CD34 in APL was highly associated with leukocytosis, hypogranular morphology, and coexpression of CD2.⁷ In addition, a high presenting WBC count (≥ 10 × 10⁹/L) was found to be associated with poor overall survival and increased rate of relapse. However, ultimately, coexpression of CD34 and HLA-DR is extremely rare in APL. The mechanism behind the atypical expression of the lymphoid markers CD2 and HLA-DR remains an area of further investigation.

At diagnosis, next-generation sequencing revealed a genetic variant of strong clinical significance: FLT3-ITD, 63-bp, detected in approximately 22 percent of alleles. FMS-like tyrosine kinase 3 (FLT3) is a proto-oncogene involved in hematopoiesis and is mainly expressed in hematopoietic organs such as bone marrow, thymus, and lymph nodes.⁸ The FLT3 gene is found in the chromosomal region 13q12.2 and encodes a membrane-bound receptor tyrosine kinase (RTK). The most common form of FLT3 mutation is an internal tandem duplication that promotes ligand-independent auto-phosphorylation and constitutive receptor tyrosine kinase activation, which has been strongly associated with leukocytosis and poor prognosis. In addition, FLT3-ITD is associated with microgranular morphology and involvement of the bcr3 breakpoint of PML.^1,8

A genetic variant, GATA2 c.121C>G (p.P41A), was also detected by NGS with allele frequencies of approximately 49 percent and 51 percent in the initial diagnostic and follow-up remission bone marrow samples, respectively. This specific missense variant involves substitution of the nucleotide G for C at position 121 of the GATA2 coding sequence. This sequence variation is predicted to result in change of amino acid at position 41 from proline to alanine near the N terminus before the zinc finger domain, which may alter GATA2 function. While additional testing to confirm the germline nature of the variant (e.g. skin biopsy) was not performed, it is highly probable to be germline in origin given its presence in about 50 percent of tested bone marrow cells before and after remission. Germline mutations in GATA2 are typically found in the zinc finger domains of the GATA2 protein and are associated with increased risk of developing myeloid neoplasms including AML.⁹ GATA2 is a tumor suppressor gene, and its inactivation by mutation and/or epigenetic silencing has been found to accelerate disease progression in APL and other forms of AML.¹⁰

Fig. 1. Morphology and ancillary study results. (A) Blasts in peripheral blood, Wright-Giemsa stain (100×). (B) Blasts on bone marrow biopsy, hematoxylin-eosin stain (40×). (C) Flow cytometry demonstrates coexpression of CD34, CD117, and HLA-DR (86 percent of analyzed cells). (D) Routine chromosome analysis demonstrates abnormal metaphases with a translocation between the long arms of chromosomes 15 and 17, t(15;17)(q24;q21). (E) Interphase FISH results are positive for t(15;17)(PML::RARA). (F) NGS reveals GATA2 c.121C>G (p.P41A) (49 percent variant allele frequency) at initial presentation. (G) Family pedigree with available information.

The GATA2 c.121C>G (p.P41A) variant was first reported in a study by Holme, et al., which investigated genetic heterogeneity in familial myelodysplasia (MDS)/AML.¹¹ The novel variant was identified in a 48-year-old female with MDS in a family with two other individuals also diagnosed with MDS. It has also been reported in an independent study of inherited cytopenias by Kager, et al., who described the variant in a 17-year-old female with moderate neutropenia and B-cell deficiency.¹² She experienced recurrent bouts of fever and oral aphthous lesions and was ultimately diagnosed with GATA2 deficiency. Several members of her family were diagnosed with cancer including MDS. The authors concluded that her symptoms were most likely attributed to her heterozygous variant (p.P41A) of GATA2.

While both studies suggest a relationship between this variant and the development of hematological disorders, neither performed functional studies to further characterize this potential association. In addition, a minor allele fraction of the GATA2 c.121C>G (p.P41A) mutation is observed in general population studies with reference to the Genome Aggregation Database (gnomAD).¹³ In gnomAD, this variant has a population frequency of heterozygotes of approximately 0.06 percent (171 of 276,088 total alleles) across individuals of all age ranges including several known to not have cancer or disease. In the ClinVar database, six labs classified this specific mutation as a variant of uncertain significance, and two labs classified it as likely benign.¹⁴ Therefore, further studies are necessary to elucidate the potential significance of this variant in predisposing to the development of hematological disorders.

Conclusion. In summary, this case exemplifies the importance of using a multimodal diagnostic approach to arrive at the final diagnosis. The results of chromosome, FISH, and NGS studies were instrumental in establishing a diagnosis as well as in identifying a germline GATA2 variant [c.121C>G (p.P41A)] in a patient with an unusual APL. The identification of this germline variant also had important implications for known family members as further testing may be necessary. To our knowledge, this is the first description of the presence of this germline variant in a case of an atypical hypogranular APL with coexpression of CD2, CD34, and HLA-DR. This report serves as a contribution to the limited available literature regarding the implications of this unique genetic variant, which remains an area of further investigation.

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Dr. An, Dr. Saxe, and Dr. Li are in the Department of Pathology and Laboratory Medicine, and Dr. Vengoechea is in the Department of Human Genetics—all at Emory University School of Medicine, Atlanta.