Acute myeloid leukemia with NUP98::RARG resembling acute promyelocytic leukemia accompanying ARID1B gene mutation

ABSTRACT

In this study, we present a case of acute myeloid leukemia characterized by the t(11;12)(p15;q13) translocation, exhibiting clinical, immunophenotypical, and morphological features consistent with acute promyelocytic leukemia (APL). The RNA sequencing analysis of the patient's bone marrow samples revealed the presence of the NUP98-retinoic acid receptor gamma (RARG) (NUP98::RARG) gene resulting from the translocation. Furthermore, the presence of a mutation in the ARID1B gene in the patient under study indicates a potential association with resistance to all-trans retinoic acid (ATRA).

KEYWORDS:

• Translocation(11;12)(p15;q13)
• acute myeloid leukemia
• acute promyelocytic leukemia
• NUP98::RARG

Introduction

Acute promyelocytic leukemia (APL) is a subtype of acute myeloid leukemia (AML) characterized by fatal coagulation abnormalities. More than 98% of patients with APL have a promyelocytic leukemia–retinoic acid receptor alpha (PML::RARA) fusion gene caused by the chromosomal translocation t (15; 17) (q22; q21), which is sensitive to therapy with ATRA and arsenic trioxide (ATO) therapy[1,2]. However, certain AML subtypes exhibit the APL phenotype and APL-like syndromes, with X::RARs fusion genes rather than the PML–RARA fusion gene [2]. In the past few years, X::RARA has been well described, including PLZF::RARA, NPM1::RARA, and STAT5B::RARA. Furthermore, retinoic acid receptor beta(RARB) and retinoic acid receptor gamma(RARG) rearrangements have been discovered to contribute to APL-like syndromes [3]. Notably, RARB and RARG share high sequence homology with RARA[4], and unlike PML::RARA fusions, most novel X::RAR fusions are ATRA or ATO resistant. In this study, we report the case of a patient with AML with a NUP98::RARG rearrangement and review our current understanding of patients with AML harboring X::RAR fusion gene.

Case description

On 22 April 2021, a 53-year-old man was referred to our department with asthenia and fever. His blood test showed a white blood cell count (WBC) of 3.23 × 10⁹/L with 87% promyelocytes, hemoglobin level (HGB) of 85 g/L, and platelet count (PLT) of 39 × 10⁹/L. His prothrombin time, activated partial thromboplastin time, and fibrinogen levels were 13.7 s (reference, 9–13 s), 27.3 s (reference, 24.2–32.8 s), and 1.57 g/L (reference, 2–4 g/L), respectively. Fibrin degradation products and D-dimer levels were 157.57 μg/mL (reference, 0–5.0 μg/mL) and 76.30 μg/mL (reference, 0–0.55 μg/ml). Morphologic examination of bone marrow (BM) smears revealed infiltration by 97.6% of hypergranular promyelocytes without Auer bodies. The nuclei were round, quasi-circular, or irregularly shaped. The leukemia cells expressed myeloperoxidase (MPO), CD117, CD13, and CD33, and partially expressed HLA-DR and CD9, but lacked the expression of CD56, cKappa, cLambda, CD3, CD4, CD8, CD7, CD5, cCD3, cCD79a, CD16, CD15, CD123, CD10, CD64, CD2, CD36, CD14, CD19, CD34, CD38, CD11b, or CD11c. APL was highly suspected as the primary diagnosis based on the clinical features, the BM morphology, and the immunophenotype. He received ATRA 40 mg/day and ATO 10 mg/day subsequently. However, both the reverse transcription-polymerase chain reaction (RT–PCR) and fluorescence in situ hybridization (FISH) failed to detect the PML::RARA transcript in the BM (Figure 1A). After treatment for 10 days, the coagulation abnormality did not improve, and differentiation syndromes did not occur. The WBC count was 1.87 × 10⁹/L, the HGB level was 65 g/L, and there was a PLT count of 24 × 10⁹/L; he developed gastrointestinal hemorrhage. We stopped the use of ATRA, and we planned to switch the treatment to a standard 3 + 7 chemotherapy schedule. However, the patient refused further treatment due to persistent gastrointestinal hemorrhage and severe pulmonary infection.

Figure 1. (A) Dual-color FISH analysis of the patient with LSI PML::RARA dual-color. The PML gene (15q24.1) was labeled as orange, and the RARA gene (17q21.1-21.2) was labeled as green. (B) Karyotype analysis showed 46, XY, t (11; 12) (p15; q13). (C) RNA sequencing using HiSeq X Ten exhibited a recurrent NUP98::RARG fusion.

The karyotype analysis revealed 46, XY, t (11; 12) (p15; q13) [5] (Figure 1B). Meanwhile, we detected WT1 mutation by RT–PCR. To search for the potential fusion gene, we used the patient’s BM samples collected at the time of diagnosis to perform RNA sequencing using HiSeq X Ten and found a recurrent NUP98::RARG fusion (Figure 1C). In addition, SPEN mutation and ARID1B mutation were identified.

Discussion

Compared to RARA rearrangement, RARG rearrangement is the second most common X::RARs. Thirty-four AML with RARG rearrangements were identified in a recent global cooperative study[6]. In addition to NUP98::RARG, the partner genes of RARG include PML::RARG, CPSF6::RARG, NPM1::RARG::NPM1, HNRNPm::RARG, and HNRNPc::RARG. Thus far, 11 patients have been reported to have NUP98::RARG fusions from a case series of 34 cases.

From a recent literature review, we evaluated all reported patients with NUP98::RARG gene rearrangement, and the detailed information of the 11 patients, including the patient reported herein, are summarized in Table 1. The morphology of the patients’ bone marrow resembled that of APL, and the most common symptoms were bleeding and spontaneous ecchymosis (8 of 11 patients [72.7%]). Half of the patients presented with coagulopathy(low fibrinogen levels and high D-dimer levels), and cytogenetic abnormalities were found in 9(81.8%) of the 11 patients. The typical karyotype abnormality is t(11;12)(p15;q13).

Table 1. The clinical and genetic feature of APL with NUP98–RARG gene rearrangement.

Case No.	Age/Sex	Typical karyotype	Gene mutations	ATRA	ATO	Chemo	Outcome	OS	Reference
1	35/M	46,XY,t(11;12) (p15;q13)	N/A	U	U	S(DA)	Sensitive to DA and achieved CR. Underwent consolidation chemotherapy followed by ASCT. Relapsed two years later and died due to an infection complication after umbilical cord blood transplantation.	730d	[20]
2	45/F	46,XX,t(11;12)(p15;q13)	WT1	R	R	U(DA)	Resistant to ATRA + ATO, died of severe blood infection with Escherichia coli six days after completing chemotherapy (DA).	35d	[5]
3	22/M	46,XY,t(11;12)(p15;q13)	WT1	R	R	R(HAA)S(DA)	Resistant to HAA but sensitive to DA. Partial remission was achieved after the first cycle of DA, and CR was reached after the second cycle.	NA	[21]
4	18/M	normal karyotype	RUNX1,WT1	U	R	R(DA)S(HAA)	Resistant to DA, but sensitive to HAA and achieved CR. Refused to receive any therapy and relapsed three months later. Died from a severe infection.	180d	[22]
5	47/F	45, X, –X, del(9) (q13q22), t(11;12)(p15;q13)	IDH2, TET2, ASXL1 TP53,WT1	R	R	S(IA)S(HIAG)	Sensitive to IA, HIAG, half-dose CAG, and HA regimen. Achieved CR, but refused allo-HSCT. Has been leukemia-free at the last (24-month) follow-up.	720d	[23]
6	32/M	46,XY,add(1)(p22),?del(9)(p22),t(11;12)(p15;q13),inc[cp18]/46,XY[2]	WT1	R	R	S(IA)	Sensitive to IA, fludarabine + cytarabine, and high doses of cytarabine. Achieved CR. Underwent allo-HSCT and remained in CR at the last (more than 24-month) follow-up.	720d	[24]
7	64/F	46,XX,t(11;12)(p15;q13)[19]/4 6, X X[2]	WT1,NRAS	R	R	NA	Resistant to ATRA + ATO, died on the second day of IA.	NA	[24]
8	10/M	46,XY,t(11;12)(p15;q13)	WT1	R	R	R(IA) S(CAG)	CR was achieved after the first cycle of CAG. Finally, the patient underwent allo-HSCT and was alive and in CR at the last (8-month) follow-up.	240d	[25]
9	39/F	46,XX,t(11;12) (p15;q13),t(15;21)(q11.1;q21)	NA	U	U	S(HCAG)	Sensitive to HCAG and achieved CR. Underwent allo-HSCT followed by maintenance with azacitidine and venetoclax, for two cycles. Remained in CR at the last (20-month) follow-up.	600d	[26]
10	33/M	normal karyotype	NA	R	U	R(DA)	Died of cerebral hemorrhage.	NA	[27]
11	53/M	46, XY, t (11; 12) (p15; q13)	WT1,SPEN, ARID1B	R	R	NA	Resistant to ATRA + ATO, died of gastrointestinal hemorrhage.	21d	Our case

N/A not available, U uncertain, S sensitive, ATO arsenic trioxide, ATRA all-trans acid; CR complete remission, DA, daunorubicin and cytarabine, F female, M male, HA homoharringtonine and cytarabine, IA idarubicin and cytarabine, No. number

All patients who underwent second-generation sequencing harbored a WT1 mutation that may play a role in treatment resistance. Owing to the small number of patients, the impact of the high frequency of WT1 mutations should be investigated in larger and more diverse cohorts in the future. In our patient, SPEN mutation and ARID1B mutation were first reported in this type of patient. ARID1B mutations have been associated with a poor prognosis. Prior studies have reported that silencing ARID1B in the APL cell line NB4 leads to impaired differentiation in response to ATRA. Furthermore, another previous study showed a higher incidence of ARID1B mutations in APL than in non-M3 AML[7]. Therefore, more attention needs to be paid to gene mutations in AML with NUP98::RARG rearrangements, to determine whether the disease has a similar mutational spectrum to APL or non-M3 AML. SPEN gene mutation is common in mature B-cell lymphomas such as diffuse large B-cell lymphoma; however, whether the mutations are involved in the presence of phenotypical APL remains to be elucidated. All patients who received ATRA + ATO induction therapy (≥7 days) showed ATRA and ATO resistance, and subsequently received AML-like induction therapy.

A prior in vitro study identified ATRA resistance in primary leukemia cells from patients with NUP98::RARG rearrangements[8]. However, an in vivo experiment found that primary murine cells transformed by the NUP98::RARG fusion were sensitive to ATRA[9]. These contradictory ATRA sensitivities may be influenced by the different genetic backgrounds of various species or by the acquisition of additional mutations. Furthermore, responses to the standard 3 + 7 regimen included IA (idarubicin 10–12 mg/m2 for 3 days, cytarabine100 mg/m2 per day for 7 days) and DA (daunorubicin 45–60 mg/m2 for 3 days, cytarabine100 mg/m2 per day for 7 days), which also were different. Regarding patient outcomes, six patients achieved complete remission (CR), and the remaining four patients died within 35 days. After achieving CR, one patient underwent autologous hematopoietic stem cell transplant (HSCT), relapsed two years later, and died due to an infection complication after umbilical cord blood transplantation. Three patients underwent allogeneic HSCT (allo-HSCT), and no relapse or death occurred during follow-up. In general, this AML entity has a high risk of early death due to the hemorrhagic features shared with APL; however, the condition benefits from non-M3 AML treatment (intensive chemotherapy and allo-HSCT).

The PML::RARG rearrangement derived from t (12; 15) (q13; q22) was identified in a 64-year-old woman with morphologically hypergranular APL. The patient went into morphological and cytogenetic remission following treatment of IA plus ATRA; however, the lack of an early response after 18 days of ATRA treatment may indicate resistance to ATRA[10].

CPSF6::RARG is the most common fusion and has been reported by several groups to present with different transcripts, including RARG::CPSF6[11–14]. None of the patients showed sensitivity to ATRA or ATO. Similarly, both NPM1::RARG::NPM1 and HNRNPC::RARG have been reported in patients with APL-like disease and are resistant to ATRA and ATO[15, 16]. Therefore, patients with X::RARG fusion AML should be treated with AML chemotherapy.

X::RARB rearrangements are rare, and TBL1XR1::RARB derived from t(3;3)(q26;q24) is the only RARB translocation that has been identified[17–19]. Patients with AML with TBL1XR1::RARB show resistance to ATRA; Chemotherapy should be more effective.

X::RARA rearrangement is common and except PML::RARA another 16 types have been identified including PLZF::RARA, NPM1::RARA, NUMA::RARA, STAT5B::RARA, PRKAR1A::RARA, BCOR::RARA, FIP1L1::RARA, OBFC2A::RARA, TBLR1::RARA, GTF2I::RARA, IRF2BP2::RARA, FNDC3B::RARA, STAT3::RARA, TFG::RARA, NUP98::RARA and TNRC18::RARA. The sensitivities to ATRA and ATO of each type are different listed in Table 2 [2].

Table 2. ATRA/ATO therapy response for X::RARs fusions.

Fusion Protein	Incidence	ATRA Response	ATO Response
PML::RARA	98% of total	Sensitive	Sensitive
PLZF::RARA	1% of total	Resistant	Resistant
NPM1::RARA	>10 cases	Sensitive	Non-determined
NUMA::RARA	1 case	Sensitive	Non-determined
STAT5B::RARA	17 cases	Resistant	Resistant
PRKAR1A::RARA	1 case	Uncertain	Uncertain
BCOR::RARA	2 cases	Resistant	Resistant
FIP1L1::RARA	2 cases	Sensitive	Non-determined
OBFC2A::RARA	1 case	Uncertain	Non-determined
TBLR1::RARA	4 cases	Resistant	Sensitive
GTF2I::RARA	1 case	Resistant	Resistant
IRF2BP2::RARA	6 cases	Sensitive	Non-determined
FNDC3B::RARA	1 case	Uncertain	Non-determined
STAT3::RARA	2 cases	Resistant	Resistant
TFG::RARA	1 case	Sensitive	Non-determined
NUP98-RARA	1 case	Uncertain	Non-determined
TNRC18-RARA	1 case	Resistant	Resistant

Conclusion

In conclusion, we confirmed a novel NUP98::RARG gene rearrangement in a patient with AML, and summarized the morphological, cytogenetic, molecular, and biological features of this disease. The condition presented clinical and morphological features similar to those of classic APL, and the typical karyotype abnormality was t(11;12)(p15;q13). Our literature review revealed that the disease is associated with a high risk of early death due to hemorrhagic features shared with APL but it shows resistance to ATRA and ATO treatment, in concordance with the poor outcomes. Patients benefit from non-M3 AML treatment (intensive chemotherapy and allo-HSCT). Therefore, when APL is present but without PML::RARA, this unusual form of AML should be considered. RNA sequencing can facilitate an early diagnosis and guide direct treatment strategies to avoid death. More attention needs to be paid to gene mutations because specific mutations can confer treatment resistance and guide targeted treatment. Whether the disease has a similar mutational spectrum to APL, non-M3 AML, or a specific one should be determined in the future, in view of the high frequency of WT1 mutations of this entity compared to APL.

Disclosure statement

No potential conflict of interest was reported by the author(s).

Additional information

Funding

The author(s) reported there is no funding associated with the work featured in this article.