Successful Treatment of Genetically Profiled Pediatric Extranodal NK/T-Cell Lymphoma Targeting Oncogenic STAT3 Mutation

Abstract

Extranodal natural killer (NK)/T-cell lymphoma (ENKTCL) is a distinct type of non-Hodgkin lymphoma predominantly observed in Asian and Latin American adult males. A 12-year-old Hispanic female diagnosed with ENKTCL was enrolled in our genomic profiling research protocol. We identified specific somatic alterations consistent with diagnosis of ENKTCL as well as oncogenic mutations in MAP2K1 and STAT3. To our knowledge, this is the first report of an immunophenotypically confirmed and genetically profiled case of ENKTCL in a female pediatric patient in the United States, including its unique treatment and favorable outcome.

INTRODUCTION

Extranodal natural killer (NK)/T-cell lymphoma (ENKTCL) is a distinct clinico-pathological entity often associated with Epstein–Barr virus (EBV) infection.[1,2] The reported overall 5-year survival rates vary but are consistently <67%, depending on cohort size, disease stage, and prognostic model. [1–4] The incidence of ENKTCL is highest in Southeast Asia and Central/South America and is predominantly observed in males.[2,5,6] ENKTCL is very uncommon in the United States and Europe, where diffuse large B-cell lymphoma is the most common non-Hodgkin lymphoma.[1] Of the cases seen in the United States, 80% are males and 20% are females, with median age ranges between 29–75 years for males and 49–54 years for females.[1] Thus, ENKTCL is exceedingly rare in a non-Asian pediatric female from the United States.

CASE DESCRIPTION

A 12-year-old Hispanic female was admitted to Children’s Hospital of Orange County for left orbital cellulitis and orbital subperiosteal abscess. The patient had history of runny nose, cough, and congestion and been diagnosed by her pediatrician with sinusitis. In the hospital, the patient underwent two functional endoscopic sinus surgeries with ethmoidectomy and drainage of left orbital subperiosteal abscesses. Pathology showed severe acute and chronic sinusitis with necrosis and abscess formation. Specimen culture was positive for Streptococcus pneumoniae 19F and diphtheroids. She was discharged to home with intravenous antibiotics. Following discharge, the patient continued to have swelling and erythema and underwent a left orbitotomy with drainage of orbital abscess. She received a total 28 days of antibiotics without significant clinical improvement.

Finally, during a fourth procedure for a left medial orbit abscess, a small amount of viable tissue was collected. The specimen demonstrated extensive necrosis with focal areas of viable tumor. The tumor tissue was characterized by large atypical lymphoid cells with irregular nuclear outlines and multiple nucleoli (Fig. 1A). The malignant cells were positive for CD2, CD3, CD4, CD56, and granzyme-B (Figs. 1B–F) by immunohistochemistry. The presence of EBV was confirmed by in situ hybridization (data not shown). The morphology and immunohistochemical profiles were consistent with ENKTCL. Metastatic evaluation revealed an orbital mass (Fig. 1G) demonstrating intracranial extension into the left frontal cortex (Fig. 1H) and straight gyrus (Fig. 1I).

Fig. 1.

Pathology and radiology. (A) Hematoxylin and eosin staining. Immunohistochemistry for (B) CD2, (C) CD3, (D) CD4, (E) CD56, (F) granzyme-B. Postcontrast T1-weighted MRI. (G) Left ethmoid tumor invading the left orbit and (H) left anterior cranial fossa. (I) Invasion of the left straight gyrus and adjacent dura.

Informed consent was obtained to enroll the patient in our clinical genomics research program. Nucleic acids from both tumor and nondiseased tissue were analyzed by whole genome sequencing at sequencing depths of 146× and 41×, respectively. The increased sequencing depth of the tumor allowed for increased assay sensitivity and variant discovery. The data were analyzed using a customized bioinformatic pipeline and subsequently contextually interpreted. Somatic analysis revealed a total of 247 coding mutations in the tumor. Structural analysis was also performed to identify copy number alterations, inversions, and translocations. Notably, EBV viral sequences were identified (data not shown) along with a partial deletion of chromosome 6q, and a nonsense mutation in PRDM1, thereby supporting a diagnosis of ENKTCL [2,5,7] (Figs. 2A and B). Oncogenic MAP2K1 (K57N) and STAT3 (N647I) mutations were also identified in this tumor (Fig. 2B). Both MAP2K1 and STAT3 mutations are annotated in the COSMIC database and their respective oncogenic effects have been experimentally validated.[8–10]

Fig. 2.

Molecular profiling data. (A) Circos plot illustrating the genomic profile. Outside-in: genes of interest, chromosome ideograms, copy number plot, and chromosomal structural aberrations. Red arrow points to loss of chromosome 6q. (B) Sanger sequence validation of mutations of interest. Altered nucleotides (N) are indicated by red arrows.

Initially the patient received three courses of modified RT-DeVIC protocol (concurrent radiotherapy with three courses of dexamethasone, etoposide, ifosamide, carboplatin).[11] Triple intrathecal chemotherapy (methotrexate, hydrocortisone, cytarabine) was added on day 1 of each course. Simultaneously, the patient received 50.4 Gy (gray) of radiation to the paranasal sinuses and left frontal lobe, delivered in 28 fractions using intensity-modulated radiation therapy. This initial treatment was followed by five cycles of a modified SMILE protocol (dexamethasone, methotrexate, ifosfamide, L-asparaginase, and etoposide), [12] consisting of triple intrathecal chemotherapy and methotrexate on day 1, ifosfamide on days 2–4, etoposide phosphate on days 2–4, asparaginase Erwinia chrysanthemi and dexamethasone on days 2–4. Due to etoposide and l-asparaginase allergies, both RT-DeVIC and SMILE regimens were modified to include etoposide phosphate and asparaginase E. chrysanthemi. After the completion of chemotherapy the patient received 1 year of therapy with daily vorinostat (300 mg orally). Side effects from the addition of vorinostat included occasional constipation, a single episode of fever, and transient elevation of serum creatinine. At the time of the submission of this manuscript (27 months after diagnosis), the patient remains in complete remission with excellent quality of life.

DISCUSSION

ENKTCL is an aggressive and locally destructive type of non-Hodgkin lymphoma that is seldom seen in the pediatric population. It is extremely rare in North America, comprising only 1.5% of all lymphomas in the United States.[6] ENKTCL is classified as nasal type when confined to the nasal cavity, and typically causes local destruction of cartilage, bone, and soft tissues. Extranasal ENKTCL impacts other organs or tissues besides the nasal cavity.[1] Overall, the prognosis for ENKTCL is poor.[1–4]

Diagnosis of ENKTCL is particularly challenging due to extensive tissue necrosis. A definitive histological diagnosis requires the identification of atypical hematopoietic cells on a background of inflammatory, necrotic, and degenerating cells.[1,6] Furthermore, ENKTCL is strongly linked to EBV, suggesting an important oncogenic role of the virus.[13,14] The exceedingly rare clinical presentation of this case warranted the combined use of both immunophenotyping and genomic profiling to arrive at an accurate diagnosis.

The oncogenic mutations identified are of therapeutic significance as they result in increased downstream activity of the MAP2K1 and JAK/STAT pathways, respectively. The MAP2K1 (K57N) mutation, which encodes the mutant MEK1 protein, is associated with resistance to small molecule inhibitors of ALK and BRAF. Furthermore, a mutation affecting the corresponding helical domain of its highly homologous signaling partner MEK2 confers resistance to the MEK inhibitor trametinib,[15] suggesting against the use of this specific therapy.

Recent genomic profiling of ENKTCL revealed oncogenic STAT3 mutations in 26% of patients, all within the SH2 domain.[16] The STAT3 N647I mutation identified in our participant also lies in the SH2 domain. This mutation was previously reported to confer increased JAK-independent signaling activity in large granular lymphocytic leukemia.[9,10] Different histone deacetylase inhibitors have been shown to inhibit oncogenic JAK/STAT signaling in hematologic malignancies.[17–20] Exposure of diffuse large B-cell lymphoma cells to panobinostat resulted in decreased STAT3 activity.[18] Furthermore, vorinostat inhibited STAT3 phosphorylation in cutaneous T-cell lymphoma cell lines.[20] Significant decreases of STAT3 phosphorylation were also observed in biopsy material from patients enrolled in a vorinostat phase IIb clinical trial,[20] thus providing rationale for the addition of vorinostat to our patient’s treatment regimen. Although we were not able to determine how vorniostat contributed to this patients outcome, attempting to target oncogenic STAT3 represents a novel precision medicine approach to treating this aggressive disease.

In this age of molecularly targeted precision medicine, a synergism of clinical, translational, and basic science research is needed in order to elucidate novel targets for therapeutic intervention. There are few disciplines where this is more pertinent than in pediatrics where the molecular underpinnings of a variety of diseases remain unknown. This case challenges the clinical paradigm of this disease and represents a unique interdisciplinary team approach to diagnose, profile, interpret, and treat a difficult adult disease occurring in a most atypical pediatric patient.

Abbreviations:

ALK

anaplastic lymphoma kinase

BRAF

v-Raf murine sarcoma viral oncogene homolog B

CD2

cluster of differentiation 2

CD3

cluster of differentiation 3

CD4

cluster of differentiation 4

CD56

cluster of differentiation 56

COSMIC

Catalogue of Somatic Mutations in Cancer

EBV

Epstein–Barr virus

ENKTCL

extranodal natural killer/T-cell lymphoma

Gy

gray

IT

intrathecal

JAK

Janus-activated kinase

MAP2K1

mitogen-activated protein kinase kinase 1

MEK

mitogen/extracellular signal-regulated kinase

PRDM1

PR domain containing 1

RT-DeVIC

radiotherapy concurrent with dexamethasone, etoposide, ifosfamide, and carboplatin

SH2

Src homology 2

SMILE

dexamethasone, methotrexate, ifosamide, L-asparaginase, and etoposide

STAT

signal transducer and activator of transcription

STAT3

signal transducer and activator of transcription 3