Education | 2023-11-07

Application:

Human research

Molecular genomics

Oncology

Solid tumors

Product:

Direct Label and Stain

Saphyr System

Amanda M. Dossat, PhD

Central nervous system (CNS) tumors pose a significant challenge in pediatric oncology, representing the most prevalent cancer type and a leading cause of cancer-related mortality in the pediatric community¹. The prognosis and treatment options for CNS tumors hinge on early and accurate diagnosis ². In recent years, the toolkit for identifying the molecular features of CNS tumors has rapidly expanded, contributing to the classification of over 100 unique CNS tumor types³.

Optical Genome Mapping (OGM) Addresses Current Challenges in Tumor Molecular Profiling

While traditional molecular profiling studies have predominantly relied on sequencing-based technologies, which reliably identify single nucleotide variants (SNVs) and insertions/deletions (INDELS), there is a need to study the contributions of structural variants (SVs) in tumorigenesis⁴. SVs are large genomic alterations that can be classified as insertions/deletions, balanced/unbalanced translocations, inversions, duplications, and copy number variations. Traditional methods (e.g., karyotyping) suffer from poor resolution and limited ability to detect SVs⁵. Furthermore, karyotype analysis requires cell culture, which poses a significant challenge in the examination of many sample types, including solid tumors. Together, these technical barriers in the study of SVs underscore the need for innovative approaches capable of comprehensive SV detection.

“Optical genome mapping identifies a novel pediatric embryonal tumor with a ZNF532::NUTM1 fusion”⁶, is a case study in the evolving landscape of tumor-associated molecular biomarkers. The study authors used OGM to uncover a unique fusion event, suspected to be the genomic driver of the patient’s brain tumor. Notably, OGM provided molecular insights that escaped detection by standard-of-care (SoC) methodologies. These insights were gained through OGM’s high-resolution detection of SVs in a genome-wide, unbiased fashion, without the need for amplification or a reference genome.

OGM Identification of SVs: Closing the Tumor Identification Gap

The impact of SV detection on a genome-wide scale extends beyond refining our understanding of tumor biology; it holds the promise of more accurate prognostication and the application of tailored treatment strategies⁴. In this case study, an 18-month-old male with neurological and developmental symptoms underwent imaging that revealed a cystic mass in the temporoparietal region of the brain. Histopathological analysis diagnosed a World Health Organization grade IV CNS embryonal tumor, which is a rare and poorly differentiated neoplasm found in the CNS of young children⁷.

Due to the poorly described nature of the embryonal tumor, the study authors explored the tumor identity using comprehensive methods, including methylation array, genome sequencing analysis, and OGM. Despite this multi-faceted approach, the only technique that identified clinically relevant events was OGM. The OGM-detected event was a unique fusion event—ZNF532::NUTM1—which the authors stated was the likely genomic driver of the malignancy.

Summary of molecular assays and associated findings:

• Methylome Profiling: methylation-based classification failed to associate the patient’s tumor with known CNS tumor subgroups (e.g., embryonal tumors, sarcomas).
• Genome sequencing: application of a germline tumor panel (~120 genes) identified two variants of unclear significance. Neither variant was associated with the patient’s tumor. Analysis of SNVs and INDELS failed to reveal any significant Tier 1 or Tier 2 somatic mutations (e.g., SMARCB1).
• OGM: detected several SVs and rearrangements, including a potentially clinically relevant fusion event between two protein-coding genes on chromosomes 15 and 18.

The SVs identified by OGM with the greatest clinical significance was the fusion of nuclear protein of the testis midline carcinoma family member 1 (NUTM1) on chromosome 15 with zinc finger protein 532 (ZNF532) on chromosome 18. This fusion event was later confirmed by orthogonal techniques (i.e., genome- and RNA-sequencing). This ZFN532:NUTM1 fusion event has been reported in adult tumors in the peripheral nervous system, yet this is the first report of this fusion in the CNS and in a pediatric patient⁶.

          NUTM1 is a protein coding gene, and NUTM1 gene fusions are often observed in malignant tumors. NUTM1 fusion partners often include a gene involved in transcription regulation and has been reported in sarcoma and hematologic malignancies in both children and adults⁸. Tumors harboring a NUTM1 mutation require multimodal treatment strategies and often fail to respond to chemotherapy⁹, underscoring the need for precise detection of the oncogenic drivers in CNS tumors.

          ZFN532 is a known protein coding gene and has been identified as a fusion partner of NUTM1, however the ZFN532::NUTM1 fusion is rare as compared to other NUTM1 fusion partners^10,11. Due to the rare nature of this fusion event, particularly within the pediatric population, the oncogenic impact of this fusion in brain tumors remains to be explored.

A Glimmer of Hope: The Future of Precision Pediatric Cancer Care

Accurate and timely diagnosis of the specific genetic drivers of pediatric brain cancer can be essential for optimizing patient outcomes and informing treatment strategies. As our knowledge of the molecular drivers of rare and poorly differentiated embryonal tumors deepens, this opens the door for mutation-specific treatment options with the potential for fewer side effects and improved duration of response. One day, we hope the armamentarium of therapeutic agents will be as diverse as the SVs in tumor DNA.

• Pediatric embryonal tumors are rare and poorly differentiated CNS neoplasms that remain a significant challenge in the identification of key features that drive their development and growth.  
• OGM detected a novel ZNF532::NUTM1 fusion, which filled a knowledge gap left by SoC methodologies and added a new dimension to our understanding of pediatric embryonal tumors.  
• In the future, the integration of OGM into routine clinical practice could result in enhanced patient outcomes in the realm of pediatric oncology.
• Screening for this or similar NUTM1 rearrangements should be considered for all patients with unclassified CNS tumors to ensure accurate diagnosis.
• As we continue to unravel the genomic mysteries of CNS tumors, we move closer to a future where every child diagnosed with brain cancer can receive the personalized care they deserve.

Click below to learn more from the study’s lead author about the impact of OGM on the genomic profiling of pediatric brain tumors.

References:

1. Ostrom, Q. T. et al. Alex’s Lemonade Stand Foundation Infant and Childhood Primary Brain and Central Nervous System Tumors Diagnosed in the United States in 2007-2011. Neuro Oncol 16 Suppl 10, x1–x36 (2015).
2. Salari, N. et al. The global prevalence of primary central nervous system tumors: a systematic review and meta-analysis. Eur J Med Res 28, 39 (2023).
3. Bornhorst, M. et al. Optical genome mapping identifies a novel pediatric embryonal tumor with a ZNF532::NUTM1 fusion. J Pathol 260, 329–338 (2023).
4. Louis, D. N. et al. The 2021 WHO Classification of Tumors of the Central Nervous System: a summary. Neuro Oncol 23, 1231–1251 (2021).
5. Luo, W. et al. NUTM1-Rearranged Neoplasms-A Heterogeneous Group of Primitive Tumors with Expanding Spectrum of Histology and Molecular Alterations-An Updated Review. Curr Oncol 28, 4485–4503 (2021).
6. Chau, N. G. et al. An Anatomical Site and Genetic-Based Prognostic Model for Patients With Nuclear Protein in Testis (NUT) Midline Carcinoma: Analysis of 124 Patients. JNCI Cancer Spectr 4, pkz094 (2020).
7. Agaimy, A. et al. Misleading Germ Cell Phenotype in Pulmonary NUT Carcinoma Harboring the ZNF532-NUTM1 Fusion. Am J Surg Pathol 46, 281–288 (2022).
8. Chien, Y.-W. et al. Primary malignant epithelioid and rhabdoid tumor of bone harboring ZNF532-NUTM1 fusion: the expanding NUT cancer family. Genes Chromosomes Cancer 58, 809–814 (2019).