A germline FLT3 variant in aplastic anemia

Abstract

FMS-like tyrosine kinase 3 (FLT3) genetic variants are commonly seen in high-grade myeloid neoplasms and are typically gain-of-function mutations associated with a proliferative disease phenotype. Inactivating FLT3 variants have been less frequently described in non-malignant, autoimmune disorders and are uncommon in aplastic anemia (AA). Herein, we report the first to our knowledge, and unusual case of a germline, gain-of-function, FLT3 variant in a patient with severe AA treated successfully with immunosuppressive therapy. Although a proposed link between dysregulated FLT3 signaling and autoimmunity has been described and could be speculated in the case of AA, it is currently unknown whether a pathogenetic connection between an activating germline FLT3 variant and AA truly exists and whether the mutation signifies a lifelong risk of disease recurrence and/or clonal evolution. However, the recognition of the FLT3 gene as subject not only to somatic but also germline mutations is the first step in interrogating its functional implications. Further study of unusual genotype-phenotype combinations, such as in the case presented, may shed light on a potential pathogenetic link.

Supplementary Information

The online version contains supplementary material available at 10.1186/s40364-024-00717-3.

To the editor,

We present an unusual case of severe aplastic anemia (SAA) in a patient harboring a gain-of-function, presumed-germline FMS-like tyrosine kinase 3 (FLT3) variant.

Case summary

A 57-year-old African American woman was incidentally found to have pancytopenia during a pre-operative workup (Table 1). Her complete blood count up to six years prior was notable for intermittent mild normocytic anemia and neutropenia. She reported a negative known family history of hematologic disorders. The initial evaluation was unrevealing (Table 2), except for a low-titer positive ANA screen without clinical evidence of active autoimmune disease. The workup for paroxysmal nocturnal hemoglobinuria (PNH) showed no evidence of a PNH clone in flow cytometric analysis. Bone marrow aspiration and biopsy revealed marrow hypocellularity (5–20%) without an increase in blasts, and the marrow karyotype was normal. Next-generation sequencing (NGS) revealed a gain-of-function FLT3 c.2039 C > T (p.Ala680Val) variant with an allele frequency (VAF) of 45.9%. No other variants were detected (NeoTYPE™ Myeloid Disorders Profile, NeoGenomics Laboratories, Inc.). The high VAF in the absence of the usual proliferative phenotype of a FLT3-mutated myeloid neoplasm raised suspicion of germline origin, which was further supported by the detection of the variant in both hematopoietic (blood) and presumably non-hematopoietic tissue (saliva) (Cairo Diagnostics, LLC). The patient received immunosuppressive therapy, and she achieved hematologic remission. A surveillance marrow biopsy one year later showed normal trilineage hematopoiesis (bone marrow cellularity of 20–50%) and persistence of the FLT3 c.2039 C > T (p.Ala680Val) variant with a VAF of 52.1%.

Table 1.

Complete blood count parameters before and at the time of diagnosis of aplastic Anemia

Timeline/Parameters	Six years before presentation	Pre-treatment initiation	One-year post-treatment	Reference range
Hemoglobin (g/L)	117	76	120	122–153
Mean Cell Volume (fL)	90.9	95.3	104.5	80–96
WBC (x109/L)	4.3	1.1	4.6	4.8–10.8
ANC (x109 /L)	1.4	0.2	1.5	1.8–7.7
ALC (x109/L)	2.3	0.9	2.6	1.0–4.8
Platelet count (x109/L)	209	13	165	150–400
Absolute reticulocyte count (x109/L)	N/A	40.50	143.0	38.4–114.8

WBC: White blood cell count; ANC: absolute neutrophil count; ALC: absolute lymphocyte count; fL: femtoliter; N/A: Not available

Table 2.

Initial evaluation of pancytopenia

Parameter	Result	Reference range
Absolute reticulocyte count (cells/mL)	52.9	38.4–114.8
Vit B12 (pmol/L)	> 1100	147.0–738.0
Folate (nmol/L)	32.0	6.8–34.0
Iron (mmol/L)	21.7	11.6–31.3
Iron binding capacity (mg/dl)	380.0	250.0-410.0
Ferritin (mg/L)	148.6	10.0-150.0
Transferrin (g/L)	3.0	2.0-3.6
Hepatitis C virus antibody	Non-reactive
Hepatitis B surface antigen	Non-reactive
HIV test	Negative
TSH (mIU/L)	0.9	0.3–4.2
Copper (mmol/L)	28.7	11.0-27.6
ANA screen	Positive
ANA titer	1:40	< 1:40
ANCA-P3	< 0.2
ANCA-MPO	< 0.2
SPEP	Negative for M-protein

TSH: thyroid-stimulating hormone; ANA: Anti-nuclear antibody; ANCA-P3: Anti-proteinase 3 antibody,;ANCA-MPO: Anti-myeloperoxidase antibody; SPEP: serum protein electrophoresis; M-protein: monoclonal protein

Discussion

Aplastic anemia (AA) is a disease characterized by peripheral cytopenia and trilineage bone marrow aplasia, with a complex pathophysiology implicating immune dysregulation, telomere attrition, and clonal hematopoiesis and a lifelong risk of clonal evolution to a myeloid neoplasm [1, 2]. Somatic FLT3 variants have not been reported in AA, but four patients with SAA harboring germline, inactivating FLT3 variants, were recently described [3]. This is the first report of a gain-of-function presumed-germline FLT3 tyrosine kinase variant in a patient with SAA.

The FLT3 gene encodes the FLT3 receptor found on hematopoietic stem cells (HSC) [4], which, when activated by the FLT3 ligand produced by bone marrow stroma cells, mediates downstream signaling to promote HSC survival, proliferation, and differentiation [5]. Variants of the FLT3 gene are typically somatic events leading to constitutive FLT3 receptor activation and are predominantly seen in acute myeloid leukemia (AML) with a proliferative phenotype. The FLT3 c.2039 C > T (p.Ala680Val) has been previously described as one such activating variant, originating from a missense mutation on the kinase domain of the FLT3 receptor [6, 7], but its discovery in this patient’s case is unusual and noteworthy. First, our patient presented with marrow hypoplasia with no evidence of an abnormal cell population, and second, the FLT3 c.2039 C > T (p.Ala680Val) variant was seen in almost 50% of the cell DNA analyzed, suggesting germline origin, subsequently corroborated by its detection in presumably non-hematopoietic tissue.

The key question raised is whether, in fact, the FLT3 genetic variant played a pathogenic role in this patient’s AA, and if so, whether this implies a lifelong risk of disease recurrence and/or clonal evolution above and beyond the risk associated with acquired AA, without germline variants. Outside hematologic malignancies, FLT3 signaling plays a role in dendritic cell (DC) development and function [8]. These antigen-presenting cells modulate T-cell immune responses and have the potential to initiate autoimmunity [9, 10]. In AA, reports of FLT3 genetic variants are limited to a recent case series of 4 patients with germline inactivating mutations [3]. These patients subsequently acquired somatic variants in the other FLT3 allele or genes encoding other phosphotyrosine receptor kinases. The authors hypothesized that a maladaptive somatic genetic rescue in response to the familial FLT3 haploinsufficiency was the underlying mechanism leading to the somatic events. However, a causal relationship between the inactivating germline FLT3 variant and AA phenotype was not proposed. Similarly to what has been suggested in autoimmune diseases [11], loss-of-function FLT3 variants and compensatory upregulation of the FLT3 ligand could lead to a dysregulated immune response manifesting as AA. It is also conceivable that a gain-of-function variant could promote DC dysregulation via constitutively active FLT3 signaling, which could trigger a T-cell-mediated attack on hematopoietic cells.

Whether there is a pathogenetic connection between the presumed germline FLT3 variant and the development of severe AA or whether the germline variant poses a lifelong risk of disease recurrence or clonal evolution remains a matter of speculation. The unexpected finding of an activating germline FLT3 variant highlights the need to further explore the functional implications of such germline variants in this gene. Careful detection of new cases should enable future studies of similarly unusual genotype-phenotype combinations to shed light on potential pathogenetic links and explore their therapeutic implications.

Electronic supplementary material

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Abbreviations

AA

Aplastic anemia

AML

Acute myeloid leukemia

DC

Dendritic Cells

HSC

Hematopoietic stem cells

FLT 3

FMS-like tyrosine kinase 3

MDS

Myelodysplastic syndrome

NGS

Next generation sequencing

VAF

Variable allele frequency

Author contributions

IM was involved in conceptualizing, editing, and reviewing the manuscript. L.C. and Am.S. wrote up and edited the main manuscript. A.S., M.G., AK.V., M.K., and M.C. contributed to the final review. All authors reviewed and approved the final manuscript.

Funding

The execution of this case report did not involve any funding.

Data availability

No datasets were generated or analysed during the current study.

Declarations

Ethics approval and consent to participate

Not applicable.

Consent for publication

Consent was obtained from the patient.

Competing interests

The authors declare no competing interests.