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Altered global histone-trimethylation code and H3F3A-ATRX mutation in pediatric GBM

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Abstract

Mutations in H3.3-ATRX-DAXX chromatin remodeling pathway have been reported in pediatric GBMs. H3.3 (H3F3A) mutations may affect transcriptional regulation by altered global histone-methylation. Therefore, we analyzed yet partly understood global histone code (H3K-4/9/27/36) trimethylation pattern in H3F3A-ATRX mutants and wild-type. H3F3A, HIST1H3B, IDH1, ATRX, DAXX and Tp53 mutations were identified by sequencing/immunohistochemistry in 27 pediatric GBMs. Global histone-methylation H3K-4/9/27/36me3 and Polycomb-protein EZH2 expression were evaluated by immunohistochemistry. H3F3A-ATRX mutation was observed in 66.7 % (18/27) of pediatric GBMs. K27M and G34R-H3F3A mutations were found in 37 % (10/27) and 14.8 % (4/27) patients respectively. G34V-H3F3A, HIST1H3B and IDH1 mutations were absent. Notably, commonest global histone-methylation mark lost was H3K27me3 (17/25, 68 %) followed by H3K4me3 (45.5 %, 10/22) and H3K9me3 (18.2 %, 4/22). Global H3K36me3 showed no loss. Most significant observation was loss of one or more histone-trimethylation mark in 80 % (20/25) pediatric GBMs. Notably, simultaneous loss of H3K27me3 and H3K4me3 were present in 7/22 (31.8 %) of pediatric GBMs. Low expression of EZH2 was found in 12/24 (50 %) of cases. However no significant correlation of loss of histone-marks or EZH2 expression with H3F3A-ATRX mutants (loss of at least one histone-marks in 87.5 % (14/16) cases) versus wild-types (loss of at least one histone-marks in 75 % (6/8) cases) was seen. The present study highlights for the first time combinatorial loss of one or more histone-trimethylation marks associated with majority of pediatric GBMs and the finding suggests significant role of histone-code in the molecular biology that underlies pediatric GBMs. Hence therapies for patients with particular combinations of histone modifications present opportunity to design innovative patient-tailored treatment protocols.

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Acknowledgements

The authors are thankful to Indian Council of Medical Research (ICMR), Neuro Sciences Centre and Department of Pathology, All India Institute of Medical Sciences, New Delhi, India for funding. The authors are also thankful to Dr. Supriya mallick, Department of Radiation Oncology, All India Institute of Medical Sciences, New Delhi, for assistance in patient follow up and Dr. Mitali Mukerji, Genomics and Molecular Medicine, (CSIR-IGIB), New Delhi for providing genomics facility for this work.

Conflict of interest

The authors declare that there is no conflict of interest.

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Authors and Affiliations

  1. Department of Pathology, All India Institute of Medical Sciences (AIIMS), New Delhi, India

    Pankaj Pathak, Prerana Jha, Suvendu Purkait, Vikas Sharma, Vaishali Suri, Mehar C. Sharma & Chitra Sarkar

  2. Genomics and Molecular Medicine, Council of Scientific and Industrial Research - Institute of Genomics and Integrative Biology (CSIR-IGIB), New Delhi, India

    Mohammed Faruq

  3. Department of Neurosurgery, All India Institute of Medical Sciences, New Delhi, India

    Ashish Suri

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  1. Pankaj Pathak
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  2. Prerana Jha
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Correspondence to Chitra Sarkar.

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Pankaj Pathak and Prerana Jha have equally contributed to this study.

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Pathak, P., Jha, P., Purkait, S. et al. Altered global histone-trimethylation code and H3F3A-ATRX mutation in pediatric GBM. J Neurooncol 121, 489–497 (2015). https://doi.org/10.1007/s11060-014-1675-z

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  • DOI: https://doi.org/10.1007/s11060-014-1675-z

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