Sex differences in methylation profiles are apparent in medulloblastoma, particularly among SHH tumors

Rachel M Moss; Natali Sorajja; Lauren J Mills; Christopher L Moertel; Thanh T Hoang; Logan G Spector; David A Largaespada; Lindsay A Williams

doi:10.3389/fonc.2023.1113121

Sex differences in methylation profiles are apparent in medulloblastoma, particularly among SHH tumors

Front Oncol. 2023 Mar 24:13:1113121. doi: 10.3389/fonc.2023.1113121. eCollection 2023.

Authors

Rachel M Moss^{1

2}, Natali Sorajja^{1

3}, Lauren J Mills^{1

4}, Christopher L Moertel^{4

5

6}, Thanh T Hoang^{7

8

9}, Logan G Spector^{1

4}, David A Largaespada^{4

6

10

11

12}, Lindsay A Williams^{1

4

6}

Affiliations

¹ Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States.
² Bioinformatics and Computational Biology, University of Minnesota, Minneapolis, MN, United States.
³ Macalester College, St. Paul, MN, United States.
⁴ Masonic Cancer Center, University of Minnesota, Minneapolis, MN, United States.
⁵ Pediatric Hematology and Oncology, Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States.
⁶ Brain Tumor Program, University of Minnesota, Minneapolis, MN, United States.
⁷ Department of Pediatrics, Division of Hematology-Oncology, Baylor College of Medicine, Houston, TX, United States.
⁸ Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX, United States.
⁹ Cancer and Hematology Center, Texas Children's Hospital, Houston, TX, United States.
¹⁰ Department of Pediatrics, University of Minnesota, Minneapolis, MN, United States.
¹¹ Department of Genetics, Cell Biology and Development, University of Minnesota School of Medicine, Minneapolis, MN, United States.
¹² Center for Genome Engineering, University of Minnesota, Minneapolis, MN, United States.

Abstract

Background: Medulloblastoma, the most common malignant pediatric brain tumor, displays marked sex differences in prevalence of the four main molecular subgroups: SHH, WNT, Group 3 and Group 4. Males are more frequently diagnosed with SHH, Group 3 and 4 tumors, which have worse prognoses than WNT tumors. Little is known about sex differences in methylation profiles within subgroups.

Methods: Using publicly available methylation data (Illumina HumanMethylation450K array), we compared beta values for males versus females. Differentially methylated positions (DMP) by sex within medulloblastoma subgroups were identified on the autosomes. DMPs were mapped to genes and Reactome pathway analysis was run by subgroup. Kaplan-Meier survival curves (Log-Rank p-values) were assessed for each sex within subgroup. MethylCIBERSORT was used to investigate the tumor microenvironment using deconvolution to estimate the abundances of immune cell types using DNA methylation data.

Results: There were statistically significant differences in sex by medulloblastoma subgroups (chi-squared p-value=0.00004): Group 3 (n=144; 65% male), Group 4 (n=326; 67% male), SHH (n=223; 57% male) and WNT (n=70; 41% male). Females had worse survival than males for SHH (p-value=0.02). DMPs by sex were identified within subgroups: SHH (n=131), Group 4 (n=29), Group 3 (n=19), and WNT (n=16) and validated in an independent dataset. Unsupervised hierarchical clustering showed that sex-DMPs in SHH did not correlate with other tumor attributes. Ten genes with sex DMPs (RFTN1, C1orf103, FKBP1B, COL25A1, NPDC1, B3GNT1, FOXN3, RNASEH2C, TLE1, and PHF17) were shared across subgroups. Significant pathways (p<0.05) associated with DMPs were identified for SHH (n=22) and Group 4 (n=4) and included signaling pathways for RET proto-oncogene, advanced glycosylation end product receptor, regulation of KIT, neurotrophic receptors, NOTCH, and TGF-β. In SHH, we identified DMPs in four genes (CDK6, COL25A1, MMP16, PRIM2) that encode proteins which are the target of therapies in clinical trials for other cancers. There were few sex differences in immune cell composition within tumor subgroups.

Conclusion: There are sexually dimorphic methylation profiles for SHH medulloblastoma where survival differences were observed. Sex-specific therapies in medulloblastoma may impact outcomes.

Keywords: medulloblastoma; methylation; pediatric and young adult cancer; sex differences; survival.

Abstract

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