Spatial heterogeneity in medulloblastoma

Abstract

Spatial heterogeneity of transcriptional and genetic markers between physically isolated biopsies of a single tumor poses major barriers to the identification of biomarkers and the development of targeted therapies that will be effective against the entire tumor. We analyzed the spatial heterogeneity of multiregional biopsies from 35 patients, using a combination of transcriptomic and genomic profiles. Medulloblastomas (MBs), but not high-grade gliomas (HGGs), demonstrated spatially homogeneous transcriptomes, which allowed for accurate subgrouping of tumors from a single biopsy. Conversely, somatic mutations that affect genes suitable for targeted therapeutics demonstrated high levels of spatial heterogeneity in MB, malignant glioma, and renal cell carcinoma (RCC). Actionable targets found in a single MB biopsy were seldom clonal across the entire tumor, which brings the efficacy of monotherapies against a single target into question. Clinical trials of targeted therapies for MB should first ensure the spatially ubiquitous nature of the target mutation.

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Figure 1: Medulloblastomas, but not glioblastomas, show reliable transcriptome-based subgroup prediction.
Figure 2: The variable intratumoral heterogeneity of somatic alterations in all tumor entities.
Figure 3: Spatial intermixing of clonal lineages.
Figure 4: Genetically distinct clonal lineages yield ON/OFF mutation patterns between spatially separated biopsies.
Figure 5: Quantification of variable genetic heterogeneity across tumor entities.
Figure 6: Genetic heterogeneity at recurrence greatly exceeds spatial heterogeneity in MB.

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Acknowledgements

The MAGIC project (M.D.T. and M.A.M.) is financially supported by Genome Canada, Genome BC, Terry Fox Research Institute, Ontario Institute for Cancer Research, Pediatric Oncology Group Ontario, funds from The Family of Kathleen Lorette and the Clark H. Smith Brain Tumour Centre, Montreal Children's Hospital Foundation, Hospital for Sick Children: Sonia and Arthur Labatt Brain Tumour Research Centre, Chief of Research Fund, Cancer Genetics Program, Garron Family Cancer Centre, B.R.A.I.N. Child, M.D.T.'s Garron Family Endowment, and the BC Childhood Cancer Parents Association. M.D.T. is supported by a Stand Up To Cancer St. Baldrick's Pediatric Dream Team Translational Research Grant (SU2C-AACR-DT1113); Stand Up To Cancer is a program of the Entertainment Industry Foundation administered by the American Association for Cancer Research. M.D.T. is also supported by The Garron Family Chair in Childhood Cancer Research, and grants from the Cure Search Foundation, the US National Institutes of Health (R01CA148699 and R01CA159859), The Pediatric Brain Tumor Foundation, The Terry Fox Research Institute, and Brainchild. This study was conducted with the support of the Ontario Institute for Cancer Research through funding provided by the Government of Ontario, as well as The Brain Tumour Foundation of Canada Impact Grant of the Canadian Cancer Society and Brain Canada with the financial assistance of Health Canada (grant 703202 to M.D.T.). This work was also supported by a Program Project Grant from the Terry Fox Research Institute (to M.D.T.), a Grand Challenge Award from CureSearch for Children's Cancer (to M.D.T.), and the PedBrain Tumor Project contributing to the International Cancer Genome Consortium, funded by German Cancer Aid (109252) and by the German Federal Ministry of Education and Research (BMBF; grants 01KU1201A and MedSys 0315416C to S.M.P. and P.L.). We acknowledge the Labatt Brain Tumour Research Centre Tumour and Tissue Repository, which is supported by B.R.A.I.N. Child and Megan's Walk (M.D.T.). M.A.M. acknowledges support from the Canadian Institutes of Health Research (CIHR; FDN-143288). M.R. is supported by a fellowship from the Dr. Mildred Scheel Foundation for Cancer Research/German Cancer Aid. F.M.G.C. is supported by the Stephen Buttrum Brain Tumour Research Fellowship, granted by the Brain Tumour Foundation of Canada. V.R. is supported by a CIHR fellowship and an Alberta Innovates–Health Solutions Clinical Fellowship. For technical support and expertise in next-generation sequencing efforts, we thank The Centre for Applied Genomics (Toronto, Ontario, Canada). We thank S. Archer for technical writing, and C. Smith for artwork.

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A.S.M., F.M.G.C., M.R., M.D.T., and M.A.M. led the study and wrote the manuscript. A.S.M. and F.M.G.C. designed, supervised, and performed bioinformatic analyses. M.R. led the collection of samples and data generation, and performed bioinformatic analyses. B.L. extracted nucleic acids, managed biobanking, and maintained the patient database. S.H., A.M.F., B.L.H., C.D., D.J.H.S., D.M.M., D.P., D.T.W.J., E.N.K., H.F., J.M., J.P., J.R., J.T., L.G., L.K.D., M.V., P.A.N., S. Agnihotri, S. Albrecht, S.C.M., S.P.-C., V.H., V.R., X. Wu, X. Wang, and Y.Y.T. provided technical and bioinformatic support. A.A., A.T., C.M., D.L., E.C., E.M., H.I.L., J.E.S., K.T., M.M., N.D., P.P., R.C., R.D.C., T.W., W.L., Y.C., and Y.L. led and performed RNA-seq and whole-genome sequencing library preparation and sequencing experiments, and performed data analyses. N.T. and Y.M. supervised bioinformatic analyses at the Genome Sciences Center. H.N. and T.G. performed whole-exome sequencing library preparation and sequencing experiments, and performed data analyses. B.R.R., C.S., C.E.H., J.L., J.S.M., N.J., P.B., R.J.P., S.D., and U.S. provided the patient samples and clinical details that made the study possible. A.H., A.J.M., A.K., D.M., E.B., G.D.B., J.T.R., M.K., P.D., P.L., R.A.M., S.J.M.J., S.M.P., and U.T. provided valuable input regarding study design, data analysis, and interpretation of results. M.D.T. and M.A.M. provided financial and technical infrastructure and oversaw the study, and served as joint senior authors and project co-leaders.

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Correspondence to Marco A Marra or Michael D Taylor.

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Morrissy, A., Cavalli, F., Remke, M. et al. Spatial heterogeneity in medulloblastoma. Nat Genet 49, 780–788 (2017). https://doi.org/10.1038/ng.3838

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