This talk will review the genomic alterations underlying malignant peripheral nerve sheath tumour (MPNST) development and progression, highlighting some established findings and analyses. It will outline the growing wealth of data from patient tumours and experimental models, mainly accessible from the NF Data Portal, and opportunities for their reuse.

Background:
Neurofibromatosis type 1 (NF1) is a common autosomal dominant neurocutaneous disorder characterized by marked phenotypic heterogeneity and extensive allelic diversity. However, genotype-phenotype correlations underlying this disorder remain incompletely defined.

Methods:
In this retrospective cohort study, germline genotype and clinical phenotype data were collected from patients with NF1. Variants were annotated using a prespecified framework incorporating structural, functional, and positional features. Associations with individual phenotypes, organ-system domains, burden scores, and latent phenotypic classes were evaluated using logistic regression and inverse probability of treatment weighting (IPTW), with XGBoost and SHAP used as complementary exploratory approaches.

Results:
Among 929 patients with NF1 (mean age, 15.1 years; 47.6% female; 74.6% de novo variants), pigmentary manifestations were most common, while PNFs and cNFs were present in 63.9% and 46.7%, respectively. SNVs were the predominant variant class (55.9%), and loss-of-function variants accounted for 76.5% of non-CNV variants. Significant associations were identified across tumor-related, skeletal, pigmentary, neurodevelopmental, and composite burden phenotypes. Missense variants were associated with a lower likelihood of cNFs (OR, 0.52), whereas non-loss-of-function variants were associated with a lower likelihood of overall PNFs (OR, 0.64) and lower total burden (OR, 0.62). Site-specific associations observed for AA2285/exon 37 and paraspinal/spinal PNF, and for AA1534/p.Arg1534Ter and optic pathway glioma. IPTW analyses showed broadly consistent directions, and XGBoost/SHAP supported the importance of positional and domain-level features across phenotypes.

Conclusion:
Genotype-phenotype associations were identified across multiple phenotypic domains in NF1, including tumor-related, skeletal, pigmentary, neurodevelopmental, and composite burden phenotypes. These findings may support more refined phenotypic stratification and individualized surveillance.

Background: Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive sarcomas, with a median survival under 5 years. Surgery remains the only treatment of established benefit, and no molecularly guided therapeutic strategies exist. The epigenetic, transcriptional, and microenvironmental drivers of MPNST progression and metastasis remain poorly understood.
Methods: We assembled the largest molecularly annotated MPNST cohort to date from 148 patients across ten institutions, with genome-wide DNA methylation profiling performed on 191 samples. Bulk RNA sequencing was performed on 95 samples, and single-nuclei RNA sequencing (snRNA-seq) was conducted on 21 MPNSTs to characterize the tumor microenvironment.
Results: Consensus clustering of methylation data identified two stable molecular subgroups (G1, G2) with biologically and clinically distinct behaviour. Subgroup identity remained consistent across primary, recurrent, and metastatic presentations in 40 longitudinal samples from 18 patients, suggesting an intrinsic tumour property. G1 tumors had shorter overall survival (17.3 vs. 43.0 months; p=0.0069) and earlier metastatic progression (median 15.7 months vs. not reached; p=0.0021) compared to patients with G2 MPNSTs. Margin-negative resection did not improve survival in G1 tumours but significantly improved G2 tumours (p=0.02). Transcriptomic analyses showed immune and inflammatory pathway enrichment in G2 MPNSTs, while G1 was characterized by proliferation and cell cycle programs. SnRNA-seq and IHC confirmed enrichment of myeloid cells and lymphocytes in G2 MPNSTs and an immune-deplete microenvironment in G1 MPNSTs.
Conclusion: G1 MPNSTs exhibit early metastatic progression and reduced overall survival that is not overcome by current therapies. Their immune-deplete microenvironment provides a biological rationale for metastasis and highlights therapeutic vulnerabilities requiring further investigation.

Background:
Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive, heterogeneous sarcomas with poor prognoses. Overlapping histological traits challenge diagnosis, hampering an integrative view of molecular pathogenesis. We hypothesized that specific combinations of tumor suppressor gene (TSG) inactivation may dictate distinct genomic evolution paths, ultimately defining distinct biological and clinical tumor identities.

Methods:
We performed comprehensive genomic (WGS) and transcriptomic (RNA-seq) analyses on 20 clinically diagnosed MPNSTs and 7 atypical neurofibromatous neoplasms of uncertain biologic potential (ANNUBPs). Point mutations, copy number variants, and structural variants were analyzed, validating copy number alterations using FISH in cell lines. We also completely re-analyzed an external dataset of 50 MPNST whole-genome and whole-transcriptome profiles, totaling 70 distinct tumor samples.

Results:
We uncovered recurrent copy-neutral loss-of-heterozygosity and distinct copy-number profiles, which were validated by FISH and reproduced in the external dataset, and showed that CDKN2A-inactivating translocations are already present in pre-malignant ANNUBPs. Finally, we identified three molecular subtypes of MPNSTs (G1-G3) based solely on their initial TSG inactivation profiles, correlating with distinct genomic identities and clinicopathological features. These analyses overcome the dominant influence of PRC2 status in MPNSTs and provide a unifying, multi-step progression model from initial TSG inactivation to stabilized genomic profiles.

Conclusions:
Each MPNST subtype may represent a distinct evolutionary pathway to malignancy initiated by specific TSG alterations. Uncovering these features, including CDKN2A alterations in pre-malignant lesions, provides a framework to improve diagnostics and advance towards personalized precision oncology treatments for NF1 patients.

Background: Patients with Neurofibromatosis type 1 (NF1) are at risk of developing devastating malignant peripheral nerve sheath tumors (MPNSTs). MPNSTs mostly arise from benign plexiform neurofibromas (PNs). As they respond poorly to treatment, they constitute the leading cause of death in NF1 patients. Thus, a deeper understanding of the processes leading to malignant transformation of PN is required to develop effective therapies. Ultimately, a two-drug strategy may reduce the chance for malignant progression of PNs that are at risk of causing problems.
Methods: Patient-derived cell lines representing different NF1-associated peripheral nerve sheath tumors were generated. Drug sensitivity and synergism was assessed using the cell lines previously generated. Immunofluorescence and immunoblotting were employed to assess treatment effects. In addition, tumor slice cultures of PNs were established and effects of one-two-punch treatment strategies were assessed using immunohistochemistry as well as single-cell transcriptomics.
Results: Combinations of senogenic and senolytic (SESE) drugs demonstrated synergistic effects against peripheral nerve sheath tumor cells with higher cytotoxicity against NF1-/- Schwann cell lines compared to control Schwann cell lines (i.e. NF1+/+, NF1+/-). SESE drug combinations were also efficacious against MPNST cells and demonstrated stronger cell cytotoxicity compared to MEK-inhibitors. Lastly, tumor slice cultures were considered a clinically relevant model system to assess novel treatments. MEK inhibition demonstrated the expected downregulation of phospho-ERK levels as assessed by immunohistochemistry and by single-cell transcriptomics (DUSP6 levels). Further analyses are ongoing.
Conclusion: SESE combinations are a novel strategy to potentially counteract the malignant transformation of NF1-associated peripheral nerve sheath tumors.