Genetic changes in refractory relapsed acute myeloid leukemia with NPM1 mutation: A case report

Abstract

BACKGROUND

Acute myeloid leukemia is often associated with gene mutation or chromosome abnormality, which is an important factor affecting prognosis. The 5-year survival rate of patients with acute myeloid leukemia without hematopoietic stem cell transplantation is low. For patients who only received chemotherapy and whose first remission lasted > 5 years, there are few reports of gene spectrum changes between relapse and initial diagnosis.

CASE SUMMARY

We report a 41-year-old woman who presented to our hospital with complaints of dizziness, poor appetite and wasting. She was diagnosed with acute myelomonocytic leukemia (M4b) with NPM1 mutation and only received chemotherapy. Her first remission lasted > 5 years. New genetic variants were detected upon relapse that may have been related to relapse and chemotherapy resistance.

CONCLUSION

Mutations in WT1 (R394fs/A387fs)/PTPN11 T73I/ETV6 S350P and JAK2 W659R may be related to relapse and chemotherapy resistance in acute myeloid leukemia.

Key Words: Acute myeloid leukemia; NPM1 mutation; Genetic variants; WT1; Case report

Core Tip: We report a patient with relapsed refractory acute myelomonocytic leukemia. Compared with the gene spectrum at initial diagnosis, new genetic variants were detected. We speculate that mutations in WT1 (R394fs/A387fs)/PTPN11 T73I/ETV6 S350P and JAK2 W659R may be related to relapse and chemotherapy resistance.

INTRODUCTION

Chemotherapy is the main treatment for acute myeloid leukemia (AML) patients who cannot undergo hematopoietic stem cell transplantation, but 5-year overall survival is < 40%[1,2]. It is known that some genetic variation or cytogenetic abnormalities are important factors affecting the prognosis of AML[3,4]. Here, we report a case of acute monocytic leukemia with normal karyotype and NPM1 mutation. The patient had complete remission with chemotherapy but relapsed 5 years later. New genetic variants and chromosomal abnormalities were detected when she relapsed. We found new gene mutations that may be related to chemoresistance of AML.

CASE PRESENTATION

Chief complaints

A 41-year-old woman presented to our hospital in July 2016 to address a 2-mo history of dizziness, poor appetite and wasting.

History of present illness

At admission, the patient was actively suffering from dizziness, headache, poor appetite, gum pain and unintentional weight loss (approximately 10 kg in the 2 mo prior).

History of past illness

In 2011, the patient had undergone hysterectomy for cervical cancer. Since it was early-stage cancer, no chemotherapy or radiotherapy was performed after the operation.

Personal and family history

The patient’s personal and family histories were unremarkable.

Physical examination

The patient had moderate anemia and slightly swollen gums. There was no sternal tenderness or superficial lymphadenopathy. Her liver and spleen were not palpable under the ribs.

Laboratory examinations

On July 16, 2019, bone marrow showed that the proportion of naive monocytes was 53%, and the proportion of promyelocytes was 18% (Figure 1A). A routine blood test indicated a white blood cell count of 19.4 × 10⁹/L (normal range: 4-10 × 10⁹/L), hemoglobin level of 87 g/L (normal range: 110-150 g/L) and platelet count of 113 × 10⁹/L (normal range: 100-300 × 10⁹/L).

Figure 1 Morphological observation of bone marrow cells (hematoxylin-eosin staining, magnification × 100). A: Before chemotherapy; B: After induction therapy; C: After maintenance treatment; D: At first recurrence; E: After one cycle of venetoclax and azacytidine therapy; F: After one cycle of cytarabine, homoharringtonine and venetoclax therapy.

Imaging examinations

Imaging examination showed no obvious abnormality.

Further diagnostic work-up

Karyotype analysis showed 46, XX [14]. The following 11 common genes showed mutations: NPM1 exon 12; DNMT3A exon 2 c.27C>T, p.P9P; TET2 exon 3 c.652G>A, p.V218M, c.3117G>A, p.S1039S; TET2 exon 9 c.4140T>C, p.H1380H; and ASXL1 exon 12 c.3759T>C, p.S1253S (Table 1).

Table 1 Gene testing before chemotherapy.

Gene	Variation content
NPM1	Exon 12
ASXL1	Exon 12 c.3759T>C; p.S1253S
DNMT3A	Exon 2 c.27C>T; p.P9P
TET2	Exon 9 c.4140T>C; p.H1380H
	Exon 3 c.652G>A; p.V218M c.3117G>A; p.S1039S
FLT3-ITD	No gene mutation was detected

FINAL DIAGNOSIS

Acute myelomonocytic leukemia (M4b) with NPM1 mutation.

TREATMENT

On July 19, 2016, the “idarubicin - cytarabine (IA)” regimen was administered, consisting of idarubicin at 10 mg for days 1-3 plus cytarabine at 0.1 g q12h on days 1-7. On August 3, 2016, bone examination showed complete remission (Figure 1B). On August 25, 2016, the IA regimen was given again. On September 18, 2016, the patient was treated with lumbar puncture and intrathecal injection of cytarabine plus dexamethasone. No abnormality was found in the cerebrospinal fluid examination. However, the patient refused hematopoietic stem cell transplantation for economic reasons. We chose high-dose cytarabine (3.0 g q12h on days 1, 3 and 5 q4w) as consolidation therapy, and four cycles of cytarabine were given starting on September 28, 2016. The minimal residual leukemia cell count was 5.23 × 10^-2 after consolidation treatment. Due to minimal residual leukemia, two courses of the “MA” regimen (mitoxantrone 10 mg days 1-3 + cytarabine 75 mg q12h days 1-7 q12w) and the “DA” regimen (daunorubicin 40 mg days 1-3 + cytarabine 75 mg q12h days 1-7 q12w) were given, starting on September 8, 2017. After the last chemotherapy treatment, bone marrow examination showed complete remission (Figure 1C). Routine blood tests were conducted every 3-6 mo.

In August 2021, the patient was re-hospitalized in our department due to recurrent leukemia (Figure 1D). The karyotype analysis of bone marrow cells showed: 46, X, t (X; 3) (p11.2; P13) [6]/46, XX [14]. Molecular pathological gene mutation reports showed mutations of the following genes: NPM1 exon 11 NM_002520:c.863_864insCCAG (p.W288fs); TET2 exon 3 NM_001127208: c.1588C>T(p.Q530*); WT1 exon 7 NM_024426:c.1180_1186delins8 (p.R394fs), NM_024426:c.1157dupC (p.A387fs); PTPN11 exon 3 NM_002834:c.218C>T (p.T73I); ETV6 exon 6 NM_001987:c.1048T>C (p.S350P); and JAK2 exon 15 NM_004972:c.1975T>C (p.W659R) (Table 2).

Table 2 Gene testing after the first recurrence.

Gene	Variation content	Variation ratio
NPM1	Exon 11 NM_002520:c.863_864insCCAG (p.W288fs)	11.8% (1276X)
TET2	Exon 3 NM_001127208:c.1588C>T (p.Q530*)	6.6% (2572X)
PTPN11	Exon 3 NM_002834:c.218C>T (p.T73I)	16.2% (2056X)
ETV6	Exon 6 NM_001987:c.1048T>C (p.S350P)	6.9% (1822X)
JAK2	Exon 15 NM_004972:c.1975T>C (p.W659R)	40.2% (1044X)
WT1	Exon 7 NM_024426:c.1157dupC (p.A387fs)	14.0% (1826X)
	Exon 7 NM_024426:c.1180_1186delins8 p.R394fs)	10.1% (1926X)

IA chemotherapy was given on September 27, 2021. On November 1, 2021, we observed 8% naive cells in the peripheral blood. A regimen of azacytidine at 100 mg on days 1-7 and venetoclax at 400 mg on days 1-28 was given on November 5, 2021. The minimal residual leukemia cell count was 5.9 × 10^-3 after the first cycle of treatment and 8.6 × 10^-3 after four cycles of treatment (Figure 1E). After seven cycles of treatment, naive cells reappeared in the peripheral blood.

OUTCOME AND FOLLOW-UP

The patient was subsequently treated with the “HA” regimen (cytarabine 0.15 g q12h days 1-7 + homoharringtonine 3.5 mg days 1-7) and the “CV” regimen (cytarabine 15 mg q12h days 1-10 + venetoclax 400 mg days 1-28) on June 10, 2022. Unfortunately, remission was not achieved (Figure 1F). At the last follow-up, the patient had pancytopenia, and the proportion of naive cells was 70%. Blood transfusion was administered.

DISCUSSION

AML is a highly heterogeneous hematological tumor, often accompanied by gene mutations and chromosomal abnormalities. According to the European LeukemiaNet, AML can be divided into low, medium and high risk[5,6]. It is known that AML with normal karyotype and NPM1 mutation without FLT3-ITD mutation has a better prognosis, but our patient also had mutations in DNMT3A, TET2 and ASXL1. According to the European LeukemiaNet risk classification (2017), this patient was classified as high risk due to the ASXL1 mutation.

After induction of remission, bone marrow transplantation was the best treatment, but the patient refused the recommendation. She relapsed 5 years later, and the gene spectrum and chromosome examination were performed again. Compared with the gene spectrum at diagnosis, WT1 (R394fs/A387fs), PTPN11 T73I, ETV6 S350P and JAK2 W659R mutations replaced the ASXL1 and DNMT3A mutations. This is the first report of mutations in WT1 (R394fs/A387fs), PTPN11 T73I, ETV6 S350P and JAK2 W659R in a patient with relapsed refractory AML. Eisfeld et al[7] reported that the combination of NPM1 and WT1 mutations is an adverse prognostic combination. Krauth et al[8] confirmed that WT1 mutations are independent adverse factors for event-free survival in AML patients.

TET2 mutation is an early event in the stepwise progression from hematopoietic stem cells to myeloid malignancy, but there is still controversy over the prognostic impact of TET2 mutation in AML. TET2 mutation might be correlated with relapse of leukemia[9-11]. JAK2 mutation has not been observed in the absence of TET2 mutations[12]. JAK2 V617F is the most common type of JAK2 mutation but occurs rarely in ML[13]. Currently, there are no reports of the JAK2 W659R mutation in AML. Alfayez et al[14] concluded that mutations in PTPN11 had deleterious effects on survival. ETV6 rearrangements often accompany other molecular mutations[15].

Routine chemotherapy was ineffective for this patient. However, azacytidine and venetoclax treatment achieved morphological remission and progression-free survival for 6 mo. We speculate that mutations in WT1 (R394fs/A387fs), PTPN11 T73I, ETV6 S350P and JAK2 W659R may be related to relapse and chemotherapy resistance.

CONCLUSION

We report a patient with relapsed refractory AML. Compared with the gene spectrum at diagnosis, new mutations were detected. We speculate that mutations in WT1 (R394fs/A387fs), PTPN11 T73I, ETV6 S350P and JAK2 W659R may be related to relapse and chemotherapy resistance. Larger studies are warranted to confirm this.