HGG-20. DIAGNOSTIC AND BIOLOGICAL ROLE OF METHYLATION PATTERNS IN REPLICATION REPAIR DEFICIENT HIGH GRADE GLIOMAS

Replication repair deficiency (RRD) is an important driving mechanism of pediatric high grade glioma (pHGG) occurring predominantly in the context of germline mutations in RRD-associated genes. Although pHGG present specific patterns of DNA methylation corresponding to driving oncogenic processes, methylation patterns have not been well studied in RRD tumors. We analyzed 52 RRD pHGG using either 450k or 850k methylation arrays. These arrays were compared with 234 PHGG driven by other genetic or epigenetic mechanisms and 10 additional pHGG samples known to be hypermutant. RRD pHGG displayed a methylation pattern corresponding to specific secondary mutations such as IDH1 and H3K27M. Strikingly, RRD pHGG lacking these known secondary mutations largely clustered together with a poorly described group previously labelled Wild type-C. Most of the hypermutant tumors clustered in a similar location suggesting undiagnosed RRD may be a driving force for tumors clustering in this location. Analysis of methylation patterns revealed that RRD pHGG displayed a unique CpG Island Demethylator Phenotype in contrast to the Methylator Phenotype described in other cancers. This effect was most concentrated at gene promotors. Prominent demethylation was observed in genes and pathways critical to cellular survival including cell cycle, gene expression, cellular metabolism and cellular organization. These data suggest that methylation profiles may provide diagnostic information for the detection of RRD pHGG. Furthermore, our findings highlight the unique natural selection pressures in these highly dysregulated, hypermutant cancers and provide novel impact of hypermutation and RRD on the cancer epigenome.

Clinical Updates and Surveillance Recommendations for DNA Replication Repair Deficiency Syndromes in Children and Young Adults

Replication repair deficiency (RRD) is a pan-cancer mechanism characterized by abnormalities in the DNA mismatch repair (MMR) system due to pathogenic variants in the PMS2, MSH6, MSH2, or MLH1 genes, and/or in the polymerase-proofreading genes POLE and POLD1. RRD predisposition syndromes (constitutional MMR deficiency, Lynch, and polymerase proofreading-associated polyposis) share overlapping phenotypic and biological characteristics. Moreover, cancers stemming from germline defects of one mechanism can acquire somatic defects in another, leading to complete RRD. Here we describe the recent advances in the diagnostics, surveillance, and clinical management for children with RRD syndromes. For patients with constitutional MMR deficiency, new data combining clinical insights and cancer genomics have revealed genotype-phenotype associations and helped in the development of novel functional assays, diagnostic guidelines, and surveillance recommendations. Recognition of non-gastrointestinal/genitourinary malignancies, particularly aggressive brain tumors, in select children with Lynch and polymerase proofreading-associated polyposis syndromes harboring an RRD biology have led to new management considerations. Additionally, universal hypermutation and microsatellite instability have allowed immunotherapy to be a paradigm shift in the treatment of RRD cancers independent of their germline etiology. These advances have also stimulated a need for expert recommendations about genetic counseling for these patients and their families. Future collaborative work will focus on newer technologies such as quantitative measurement of circulating tumor DNA and functional genomics to tailor surveillance and clinical care, improving immune surveillance; develop prevention strategies; and deliver these novel discoveries to resource-limited settings to maximize benefits for patients globally.

A Validated Highly Sensitive Microsatellite Instability Assay Accurately Identifies Individuals Harboring Biallelic Germline PMS2 Pathogenic Variants in Constitutional Mismatch Repair Deficiency

BACKGROUND

Constitutional mismatch repair deficiency (CMMRD) is a rare and extraordinarily penetrant childhood-onset cancer predisposition syndrome. Genetic diagnosis is often hampered by the identification of mismatch repair (MMR) variants of unknown significance and difficulties in PMS2 analysis, the most frequently mutated gene in CMMRD. We present the validation of a robust functional tool for CMMRD diagnosis and the characterization of microsatellite instability (MSI) patterns in blood and tumors.

METHODS

The highly sensitive assessment of MSI (hs-MSI) was tested on a blinded cohort of 66 blood samples and 24 CMMRD tumor samples. Hs-MSI scores were compared with low-pass genomic instability scores (LOGIC/MMRDness). The correlation of hs-MSI scores in blood with age of cancer onset and the distribution of insertion-deletion (indel) variants in microsatellites were analyzed in a series of 169 individuals (n = 68 CMMRD, n = 124 non-CMMRD).

RESULTS

Hs-MSI achieved high accuracy in the identification of CMMRD in blood (sensitivity 98.5% and specificity 100%) and detected MSI in CMMRD-associated tumors. Hs-MSI had a strong positive correlation with whole low-pass genomic instability LOGIC scores (r = 0.89, P = 2.2e-15 in blood and r = 0.82, P = 7e-3 in tumors). Indel distribution identified PMS2 pathogenic variant (PV) carriers from other biallelic MMR gene PV carriers with an accuracy of 0.997. Higher hs-MSI scores correlated with younger age at diagnosis of the first tumor (r = -0.43, P = 0.011).

CONCLUSIONS

Our study confirms the accuracy of the hs-MSI assay as ancillary testing for CMMRD diagnosis, which can also characterize MSI patterns in CMMRD-associated cancers. Hs-MSI is a powerful tool to pinpoint PMS2 as the affected germline gene and thus potentially personalize cancer risk.

Update on Pediatric Cancer Surveillance Recommendations for Patients with Neurofibromatosis Type 1, Noonan Syndrome, CBL Syndrome, Costello Syndrome, and Related RASopathies

Neurofibromatosis type 1 (NF1), Noonan syndrome, and related syndromes, grouped as RASopathies, result from dysregulation of the RAS-MAPK pathway and demonstrate varied multisystemic clinical phenotypes. Together, RASopathies are among the more prevalent genetic cancer predisposition syndromes and require nuanced clinical management. When compared with the general population, children with RASopathies are at significantly increased risk of benign and malignant neoplasms. In the past decade, clinical trials have shown that targeted therapies can improve outcomes for low-grade and benign neoplastic lesions but have their own challenges, highlighting the multidisciplinary care needed for such individuals, specifically those with NF1. This perspective, which originated from the 2023 American Association for Cancer Research Childhood Cancer Predisposition Workshop, serves to update pediatric oncologists, neurologists, geneticists, counselors, and other health care professionals on revised diagnostic criteria, review previously published surveillance guidelines, and harmonize updated surveillance recommendations for patients with NF1 or RASopathies.

DNA mismatch and damage patterns revealed by single-molecule sequencing

Mutations accumulate in the genome of every cell of the body throughout life, causing cancer and other diseases1,2. Most mutations begin as nucleotide mismatches or damage in one of the two strands of the DNA before becoming double-strand mutations if unrepaired or misrepaired3,4. However, current DNA-sequencing technologies cannot accurately resolve these initial single-strand events. Here we develop a single-molecule, long-read sequencing method (Hairpin Duplex Enhanced Fidelity sequencing (HiDEF-seq)) that achieves single-molecule fidelity for base substitutions when present in either one or both DNA strands. HiDEF-seq also detects cytosine deamination-a common type of DNA damage-with single-molecule fidelity. We profiled 134 samples from diverse tissues, including from individuals with cancer predisposition syndromes, and derive from them single-strand mismatch and damage signatures. We find correspondences between these single-strand signatures and known double-strand mutational signatures, which resolves the identity of the initiating lesions. Tumours deficient in both mismatch repair and replicative polymerase proofreading show distinct single-strand mismatch patterns compared to samples that are deficient in only polymerase proofreading. We also define a single-strand damage signature for APOBEC3A. In the mitochondrial genome, our findings support a mutagenic mechanism occurring primarily during replication. As double-strand DNA mutations are only the end point of the mutation process, our approach to detect the initiating single-strand events at single-molecule resolution will enable studies of how mutations arise in a variety of contexts, especially in cancer and ageing.

Neurocognitive outcome in children with sensorineural hearing loss after treatment of malignant embryonal brain tumors

2029

Background: Neurological side effects associated with childhood brain tumors and their treatments contribute to long term neurocognitive morbidity. The aims of this study were to identify the incidence of sensorineural hearing loss (SNHL) in a large sample of children treated for malignant brain tumors, and to evaluate the potential relationship between SNHL and intellectual functioning following the completion of treatment. Methods: We conducted a prospective follow-up study at a single center with review of 119 patients treated for embryonal brain tumors at the Hospital for Sick Children, between 1996-2015, to analyze the impact of significant SNHL (Chang > 2b) on intellectual function. Hearing was assessed post-treatment (median age: 13.5y (+4.5)) and the median age for neurocognitive testing was 12.8y (+ 4.1). The median interval from time of diagnosis was 5.8y (+ 3.7). Results: Severe SNHL was identified in half the patients (50.4%, n = 60/119). We identified a subset of patients (n = 61) who had assessments of intellectual function. In this cohort, intellectual function was significantly poorer in the group with severe SNHL, even after controlling for the effect of craniospinal radiation (severe SNHL 22.4 Gy + 13.3, no or mild hearing loss 20.4 Gy +12.8) and boost dose and volume. Children experiencing severe SNHL had lower overall IQ (severe SNHL 72.4 + 16.6; no/mild hearing loss 92.0 + 20.5) p < 0.001 and in significantly lower verbal comprehension (severe SNHL 78.7 + 15.9; no/mild hearing loss 94.7 + 13.8) p < 0.001, and working memory (severe SNHL 78.2+ 17.6; no/mild hearing loss 94.8 + 16.4) p < 0.001, scores. Conclusions: Hearing loss is a much more significant complication in children with embryonal brain tumors than previously estimated. We show the profound impact of hearing loss on intellectual deficit in children. Namely, patients with severe SNHL have difficulty using and understanding verbal language, and they have a reduced ability to concentrate and manipulate information in short-term memory. Our results have implications on future trial designs and follow-up of children treated for embryonal brain tumors.

Abstract 3552: Subgroup-specific pattern of recurrence in medulloblastoma

Background: Medulloblastoma constitutes the most common malignant brain tumor of childhood. Although multimodel treatment strategies, encompassing surgery, chemotherapy, and radiation, results in up to 80% five-year overall survival, recurrent medulloblastoma is almost always uniformly fatal. Recent integrated genomic studies have shown that medulloblastoma comprises 4 clinical and biologically distinct variants. We sought to delineate subgroup-specific differences in recurrent medulloblastoma.

Methods: We identified a discovery cohort of all recurrent medulloblastomas at the Hospital for Sick Children between 1994-2012, and subgrouped cases using nanoString. Clinical details were ascertained via retrospective chart review. Our findings were confirmed through analysis of an independent validation cohort of 85 recurrences. Primary and recurrent matched pairs were evaluated where possible.

Results: Twenty-nine recurrent cases were identified, ten with a local recurrence within the tumor bed only, and 19 recurred with metastases. Notably, SHH tumors recurred more frequently in the tumor bed (8/11, 73%) whereas Group 3 and Group 4 developed with metastatic relapses more frequently (16/18, 89%; p&lt;0.01). Late recurrences were observed more commonly in Group 4 cases with a mean time to recurrence of 3.2 years compared to under two years for both SHH and Group 3 (p&lt;0.004), with a tendency to a prolonged interval to death post-recurrence in Group 4 cases (p=0.07). Spinal metastases in the absence of supratentorial metastases were observed in three non-SHH recurrences. The presence of metastases at diagnosis and histology were not predictive factors of recurrence site. In an independent validation cohort of 85 recurrences, 13 recurrences appeared in the tumor bed only of which nine were SHH and 72 recurred with metastases. Of these metastatic relapses, only three SHH tumors were observed, while 36 and 33 belonged to Group 3 or Group4 (p&lt;0.001), respectively. Strikingly, in all instances where matched primary and recurrent pairs were available, the subgroup affiliation remained stable at recurrence.

Conclusions: Significant differences in the pattern of recurrence exist across medulloblastoma subgroups. Longer surveillance periods across the entire neuro-axis may be required for Group 4 patients even in the absence of local tumor bed or supratentorial recurrence. Intensified local therapy should be considered upon initial treatment for SHH patients.

Citation Format: Vijay Ramaswamy, Marc Remke, Eric Bouffet, David Shih, Claudia Faria, Ulrich Schüller, Sri Gururangan, Roger McLendon, Nada Jabado, Adam Fontebasso, Sandra Dunn, Joanna Triscott, Cynthia Hawkins, Uri Tabori, Kari Codispoti, Roger Packer, Stefan M. Pfister, Andrey Korshunov, Michael D. Taylor. Subgroup-specific pattern of recurrence in medulloblastoma. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 3552. doi:10.1158/1538-7445.AM2013-3552

Abstract 3460: Genome-wide copy number analysis reveals novel somatic mutations associated with choroid plexus tumorigenesis

Choroid plexus carcinomas (CPCs) are aggressive pediatric neoplasms accounting for less than 1% of brain tumors, but representing more than 10% of brain tumors in children under 1 year of age. CPCs are frequently observed in the context of the Li-Fraumeni Syndrome (LFS), yet this association has not been fully elucidated. The genetic mechanisms leading to this disease are poorly understood; however, we have recently demonstrated that TP53 status and total structural variation are correlated with tumor subtype and clinical outcome in choroid plexus tumor (CPT) patients, distinguishing between individuals with CPC and choroid plexus papilloma (CPP), a benign tumor with a more favorable prognosis. We set out to characterize genomic regions in which copy number variation and gene expression changes are uniquely associated with CPC tumors in order to identify genes that may serve as markers in tumor diagnosis and prognosis.

DNA and RNA from 59 choroid plexus tumors (CPC, n=29 and CPP, n=30) and two samples of normal choroid plexus tissue were obtained from a multi-institutional tissue and clinical database. We conducted high-resolution copy number alteration (CNA) and gene expression analysis for each tumor sample using highly dense microarrays (Affymetrix SNP 6.0 and Exon 1.0 ST array, respectively). DNA microarray data was segmented using a Hidden Markov Model (HMM) approach. Statistical analysis was carried out using Partek Genomics Suite in which CNAs and gene expression changes between CPC, CPP, and normal choroid plexus samples were contrasted. We identified 14 CPC-unique loci harboring CNAs with corresponding gene expression changes (p&gt;0.05). We observed that CNAs were found at loci where cancer genes with well-characterized oncogenic functions have been previously identified (1p13.2, 1p13.3, 1p21.3, 1p22.1 and 5q13.3). Furthermore, more than 90% of tumors with copy number alterations and expression changes at these five loci also harbored mutant TP53.

These observations suggest involvement of several genes in the malignant progression of CPCs, which may help elucidate the aggressiveness and poor clinical outcome of this tumor subtype compared to the more favorable CPP. Further analysis of CNAs and expression at these loci in the context of TP53 mutations, will provide a more refined genetic profile that will facilitate diagnosis of CPTs and aid in predicting patient outcome.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3460. doi:10.1158/1538-7445.AM2011-3460