Unusual presentation of pediatric precursor B-cell acute lymphoblastic leukemia with bulky mediastinal mass with KRAS mutation and CDKN2A/2B deletions: A case report

INTRODUCTION

Acute lymphoblastic leukemia (ALL) is the most common childhood malignancy, accounting for nearly one-quarter of all pediatric cancers.^[1,2] Approximately 85% of pediatric ALL cases arise from B-cell lineage, 10–15% from T-cell lineage, and fewer than 1% from natural killer (NK) cells.^[2] Common clinical features at presentation include fever, bleeding manifestations, musculoskeletal pain, hepatomegaly (reported in ~64%), and splenomegaly (~61%).^[3]

Less commonly, ALL may present with a mediastinal mass causing superior vena cava obstruction or superior mediastinal syndrome, a presentation typically associated with T-cell ALL (T-ALL) or T-cell lymphoblastic lymphoma due to thymic involvement.^[4,5] Presentation of precursor B-cell ALL (B-ALL) with a bulky mediastinal mass is distinctly rare. The presence of high-risk molecular alterations such as KRAS mutation and CDKN2A/CDKN2B deletions, as identified in our patient, may contribute to aggressive disease biology and atypical clinical presentation.^[6]

CASE REPORT

A 12-year-old boy presented to the pediatric emergency department with a 1-month history of progressive abdominal distension and generalized weakness, accompanied by 4–5 days of right-sided facial swelling and 2 days of bilateral pedal edema. Physical examination revealed multiple cervical lymph nodes and distended neck veins. Respiratory examination demonstrated markedly reduced air entry on the right side. Abdominal examination showed hepatosplenomegaly and shifting dullness suggestive of ascites.

Initial laboratory evaluation revealed pancytopenia with hemoglobin 7.7 g/dL, leukocyte count 72,370/µL, and platelet count 81,000/µL. Peripheral blood smear demonstrated 67% circulating blasts. Contrast-enhanced computed tomography of the thorax [Figure 1] revealed a bulky anterior mediastinal mass measuring approximately 14.8 cm in craniocaudal extent (axial dimensions 11.8 × 7.4 cm), associated with a right-sided pleural effusion.

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Figure 1:

A 12-year-old boy presenting with breathlessness, diagnosed with precursor B-cell acute lymphoblastic leukemia. (a) Contrast-enhanced computed tomography (CT) thorax, lung window, shows a bulky anterior mediastinal mass with massive right-sided pleural effusion and associated lung compression. (b) Contrast-enhanced CT thorax, mediastinal window, demonstrates a large anterior mediastinal soft-tissue mass measuring approximately 11.8 × 7.4 × 14.8 cm, causing mediastinal widening and compression of adjacent structures.

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Given the features of mediastinal syndrome, high-dose corticosteroids were initiated promptly after obtaining peripheral blood for diagnostic flow cytometry, in line with emergency management recommendations.^[3,5] Ten-color flow cytometry revealed blasts positive for CD19, CD10, cytoplasmic CD79a, surface CD22, human leukocyte antigen-DR, CD34, and terminal deoxynucleotidyl transferase, confirming precursor B-ALL.

Conventional cytogenetics demonstrated a normal male karyotype (46, XY), and multiplex polymerase chain reaction (PCR) for common ALL fusion transcripts was negative. Comprehensive leukemia panel-targeted NGS covering 141 genes identified deletions in CDKN2A and CDKN2B, along with a KRAS missense mutation with variant allele frequency of 12.73% [Figure 2]. CDKN2A and CDKN2B alterations were detected as copy number deletions, and hence, variant allele frequency was not.

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Figure 2:

A 12-year-old boy with precursor B-cell acute lymphoblastic leukemia. Targeted next-generation sequencing results demonstrate a KRAS p.Gly12Asp missense mutation with a variant allele frequency of 12.73% and copy-number deletions involving CDKN2A/CDKN2B (40.78 kb).

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Such alterations are associated with high-risk disease biology in childhood ALL.^[6-8] Sequencing was performed with an average depth of approximately 600×, with > 99% of the targeted regions achieving full coverage. Raw sequencing data were obtained in FASTQ format. Reads underwent quality control and adapter/low-quality trimming before alignment. Trimmed reads were aligned to the GRCh37/hg19 reference genome using Burrows–Wheeler Alignermaximal exact match, producing Binary Alignment Map-format alignment files, followed by marking of duplicate reads to avoid PCR artifact bias. Somatic single-nucleotide variants (SNVs) and small insertions/deletions (INDELs) were called using GATK Mutect2, while copy-number variants (CNVs) were identified through read-depth (coverage)-based algorithms. Finally, all variants (SNVs, INDELs, CNVs) were annotated using ClinVar, COSMIC, gnomAD, and OncoMD databases to assess clinical and oncogenic relevance.

Ultrasonography of the abdomen showed hepatosplenomegaly, bilateral nephromegaly with increased echogenicity, moderate ascites, and pleural effusion. Echocardiography revealed moderate pericardial effusion with preserved left ventricular systolic function. Ophthalmologic examination demonstrated retinal hemorrhages and Roth spots, consistent with leukemic involvement.

The overall presentation was consistent with high-risk B-ALL with extensive extramedullary disease. Laboratory findings suggested tumor lysis syndrome, and the patient received rasburicase as per standard guidelines.^[7]

Following stabilization and informed consent, induction chemotherapy was initiated using the modified BFM 2009 protocol. Day 8 steroid response was poor, a known adverse prognostic factor.^[9] However, day 15 minimal residual disease (MRD) assessment by flow cytometry was negative (<0.01%). Induction was complicated by methicillin-resistant coagulase-negative Staphylococcus sepsis, which resolved with appropriate antibiotics.

End-of-induction (day 33) and subsequent day 78 MRD assessments remained negative. Given poor steroid response and adverse molecular features, treatment was escalated to high-risk consolidation (HR block) in accordance with BFM protocol recommendations.^[9] The patient remains in complete remission and is tolerating maintenance therapy well.

DISCUSSION

B-ALL is the most common pediatric malignancy, but is rarely considered in the differential diagnosis of a malignant mediastinal mass in children.^[1,2] Anterior mediastinal tumors most commonly arise from thymic, lymphoid, germ cell, or thyroid origins.^[4] Mediastinal syndrome constitutes an oncologic emergency requiring urgent corticosteroid therapy to prevent cardiorespiratory compromise.^[5]

Despite excellent outcomes in pediatric B-ALL, with survival exceeding 90%, adult outcomes remain inferior.^[10] Favorable cytogenetic subtypes such as high hyperdiploidy and ETV6– RUNX1 fusion predominate in pediatric disease, whereas adverse lesions, including BCR–ABL1 are more frequent in adults.^[11] Rearrangements involving KMT2A (MLL) are characteristic of infant ALL and confer poor prognosis.^[12]

Multiplex reverse-transcription (RT) PCR was performed using a standardized leukemia fusion transcript panel designed to detect the most common recurrent genetic rearrangements in ALL. Such panels are reported to have a diagnostic sensitivity exceeding 95% and specificity approaching 100% for the detection of canonical fusion transcripts, including ETV6–RUNX1, BCR–ABL1, TCF3– PBX1, and KMT2A rearrangements, when present at diagnostic levels. A negative result does not exclude the presence of cryptic, rare, or novel genetic alterations beyond the panel coverage. Genome-wide approaches such as NGS, SNP arrays, and gene expression profiling have significantly improved risk stratification and biological understanding of ALL.^[13-15]

In a study by Zhang et al,^[16] the most prevalent driver oncogenes with mutation frequencies exceeding 5% in childhood ALL included KRAS (8.76%), NRAS (6.4%), FLT3 (5.7%), and KMT2D (5%). Among B-cell ALL cases , KRAS, NRAS, and FLT3 emerged as the most commonly mutated genes. In contrast, T-ALL was characterized by frequent mutations in NOTCH1 (23.1%), FBXW7 (23.1%), and PHF6 (11.5%).

Proto-oncogenes of the RAS family (HRAS, KRAS, and NRAS) encode 21-kDa guanosine nucleotide-binding proteins that play a critical role in transducing signals from growth factor receptors to downstream effectors involved in cell proliferation and survival. RAS proteins function as molecular switches, cycling between an active guanosine triphosphate (GTP)-bound state and an inactive guanosine diphosphate-bound state. Oncogenic mutations in RAS disrupt its intrinsic GTPase activity, leading to constitutive activation by locking the protein in its GTP-bound form, independent of upstream growth factor stimulation.

The TP53 gene, commonly referred to as p53, is a well-established tumor suppressor that regulates critical cellular processes such as apoptosis, cell cycle arrest, and senescence in response to stress signals, including DNA damage. In ALL, the p53 pathway is frequently inactivated, not only through direct mutations in TP53, but also through loss-of-function alterations in the CDKN2A locus, which are associated with poor prognosis. The CDKN2A gene encodes two distinct tumor suppressor proteins, ARF and p16 INK4a, both of which play key roles in cell cycle regulation by inhibiting cyclin-dependent kinase (CDK)-mediated phosphorylation of the retinoblastoma protein. In addition to genetic alterations, CDKN2A and related tumor suppressor genes may also be epigenetically silenced through promoter hypermethylation, further contributing to leukemogenesis.

RAS pathway mutations (KRAS, NRAS, HRAS) are among the most common somatic alterations in childhood B-ALL and are associated with relapse and treatment resistance.^[17] Loss of CDKN2A/CDKN2B disrupts cell-cycle control and p53 pathway regulation, correlating with inferior outcomes.^[18] Targeted MEK inhibition has shown promising activity in relapsed RAS-mutated ALL.^[17]

Only a handful of pediatric and adolescent B-ALL cases presenting with mediastinal mass have been reported [Table 1], all demonstrating male predominance and diagnostic challenges.^[19-22]

CONCLUSION

Pediatric B-ALL presenting with a mediastinal mass is exceptionally rare and may clinically mimic T-cell malignancies or other small round blue cell tumors. Accurate diagnosis requires integration of immunophenotyping, cytogenetics, and advanced molecular diagnostics. Identification of high-risk alterations such as KRAS mutation and CDKN2A/CDKN2B deletions contributes to risk stratification and may inform treatment intensification within established protocol-based frameworks.

Emerging therapies, including immunotherapy, molecularly targeted agents, and refined risk-adapted chemotherapy, are reshaping pediatric ALL management. Integration of NGS into routine diagnostics is crucial for optimal risk stratification and individualized therapy in such atypical presentations.