Home   >   CSC-OpenAccess Library   >    Manuscript Information
Gene Expression Changes Associated with Developing Resistance to Diffuse Intrinsic Pontine Glioma Treatments
Laura K. Harris
Pages - 40 - 57     |    Revised - 30-11-2021     |    Published - 31-12-2021
Volume - 14   Issue - 3    |    Publication Date - December 2021  Table of Contents
Panobinostat, DIPG, GSEA, Meta-analysis, Gene Expression.
Background: Diffuse Intrinsic Pontine Glioma (DIPG) is a highly lethal pediatric brainstem tumor with limited treatment options. This work is the first to analyze differential gene expression across DIPG treatments to use a Gene Set Enrichment Analysis (GSEA)-based meta-analysis approach in identifying expression changes potentially contributing to the development of therapeutic resistance.

Methods: This work defines 14 gene signatures representing six individual and panobinostat combination treatments of DIPG patient-derived cell cultures. GSEA is used to define positive and negative panobinostat gene panels from GSEA-identified leading-edge genes using two panobinostat signatures. GSEA then is used to verify enrichment and leading-edge gene membership of panobinostat panels in two independent panobinostat signatures. Analysis is then extended to five individual and five panobinostat combination signatures. Genes most associated with treatment resistance are predicted by intersecting membership of GSEA-identified leadingedges across signatures.

Results: Significant enrichment is observed between panobinostat treatment identification signatures, from which the positive (25 genes) and negative (35 genes) panobinostat panels are defined. Non-random significant enrichment is observed between panobinostat panels and verification signatures, from which 17 over- and 30 under-expressed genes are shared across leading-edges. Considering other DIPG treatments individually and in combination with panobinostat, significant non-random enrichment is observed across treatment signatures, except 5-azacytidine, for the negative panobinostat panel. Six negative panobinostat panel genes, PHF19, ASCL1, KCNK2, EBP, ITPRIPL1, and LIN9, are found across treatment signature leading-edges regardless of treatment mechanism of action or combination with panobinostat.

Conclusion: This meta-analysis identifies gene expression changes associated with DIPG. treatment. These changes may contribute to developing therapeutic resistance.
Borsuk, R., Zhou, L., Chang, W.-i., Zhang, Y., Prabhu, V., Allen, J., Tapinos, N., Lulla, R., & El-Deiry, W. (2021). HGG-42. Pediatric H3K27M Mutant Diffuse Intrinsic Pontine Glioma (DIPG) Shows Robust Response to Imipridone based combination Therapy. Neuro-Oncology, 23(Supplement_1), i26-i26. https://doi.org/10.1093/neuonc/noab090.106.
Bracken, A. P., Brien, G. L., & Verrijzer, C. P. (2019). Dangerous liaisons: interplay between SWI/SNF, NuRD, and Polycomb in chromatin regulation and cancer. Genes Dev, 33(15-16), 936-959. https://doi.org/10.1101/gad.326066.119.
Chen, L. H., Pan, C., Diplas, B. H., Xu, C., Hansen, L. J., Wu, Y., Chen, X., Geng, Y., Sun, T., Sun, Y., Zhang, P., Wu, Z., Zhang, J., Li, D., Zhang, Y., Wu, W., Wang, Y., Li, G., Yang, J., . . . Zhang, L. (2020). The integrated genomic and epigenomic landscape of brainstem glioma. Nat Commun, 11(1), 3077. https://doi.org/10.1038/s41467-020-16682-y.
Choi, S. A., Lee, C., Kwak, P. A., Park, C. K., Wang, K. C., Phi, J. H., Lee, J. Y., Chong, S., & Kim, S. K. (2019). Histone deacetylase inhibitor panobinostat potentiates the anti-cancer effects of mesenchymal stem cell-based sTRAIL gene therapy against malignant glioma. Cancer Lett, 442, 161-169. https://doi.org/10.1016/j.canlet.2018.10.012.
Clough, E., & Barrett, T. (2016). The Gene Expression Omnibus Database. Methods Mol Biol, 1418, 93-110. https://doi.org/10.1007/978-1-4939-3578-9_5.
Deng, Q., Hou, J., Feng, L., Lv, A., Ke, X., Liang, H., Wang, F., Zhang, K., Chen, K., & Cui, H. (2018). PHF19 promotes the proliferation, migration, and chemosensitivity of glioblastoma to doxorubicin through modulation of the SIAH1/beta-catenin axis. Cell Death Dis, 9(11), 1049. https://doi.org/10.1038/s41419-018-1082-z.
Ehteda, A., Simon, S., Franshaw, L., Giorgi, F. M., Liu, J., Joshi, S., Rouaen, J. R. C., Pang, C. N. I., Pandher, R., Mayoh, C., Tang, Y., Khan, A., Ung, C., Tolhurst, O., Kankean, A., Hayden, E., Lehmann, R., Shen, S., Gopalakrishnan, A., . . . Ziegler, D. S. (2021). Dual targeting of the epigenome via FACT complex and histone deacetylase is a potent treatment strategy for DIPG. Cell Rep, 35(2), 108994. https://doi.org/10.1016/j.celrep.2021.108994.
El-Khouly, F. E., Veldhuijzen van Zanten, S. E. M., Santa-Maria Lopez, V., Hendrikse, N. H., Kaspers, G. J. L., Loizos, G., Sumerauer, D., Nysom, K., Pruunsild, K., Pentikainen, V., Thorarinsdottir, H. K., Rutkauskiene, G., Calvagna, V., Drogosiewicz, M., Dragomir, M., Deak, L., Kitanovski, L., von Bueren, A. O., Kebudi, R., . . . van Vuurden, D. G. (2019). Diagnostics and treatment of diffuse intrinsic pontine glioma: where do we stand? J Neurooncol, 145(1), 177-184. https://doi.org/10.1007/s11060-019-03287-9.
Ershov, P., Kaluzhskiy, L., Mezentsev, Y., Yablokov, E., Gnedenko, O., & Ivanov, A. (2021). Enzymes in the Cholesterol Synthesis Pathway: Interactomics in the Cancer Context. Biomedicines, 9(8). https://doi.org/10.3390/biomedicines9080895.
Fortin, J., Tian, R., Zarrabi, I., Hill, G., Williams, E., Sanchez-Duffhues, G., Thorikay, M., Ramachandran, P., Siddaway, R., Wong, J. F., Wu, A., Apuzzo, L. N., Haight, J., You-Ten, A., Snow, B. E., Wakeham, A., Goldhamer, D. J., Schramek, D., Bullock, A. N., . . . Mak, T. W. (2020). Mutant ACVR1 Arrests Glial Cell Differentiation to Drive Tumorigenesis in Pediatric Gliomas. Cancer Cell, 37(3), 308-323 e312. https://doi.org/10.1016/j.ccell.2020.02.002.
Harutyunyan, A. S., Chen, H., Lu, T., Horth, C., Nikbakht, H., Krug, B., Russo, C., Bareke, E., Marchione, D. M., Coradin, M., Garcia, B. A., Jabado, N., & Majewski, J. (2020). H3K27M in Gliomas Causes a One-Step Decrease in H3K27 Methylation and Reduced Spreading within the Constraints of H3K36 Methylation. Cell Rep, 33(7), 108390. https://doi.org/10.1016/j.celrep.2020.108390.
Huang da, W., Sherman, B. T., & Lempicki, R. A. (2009). Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc, 4(1), 44-57. https://doi.org/10.1038/nprot.2008.211.
Jain, S. U., Do, T. J., Lund, P. J., Rashoff, A. Q., Diehl, K. L., Cieslik, M., Bajic, A., Juretic, N., Deshmukh, S., Venneti, S., Muir, T. W., Garcia, B. A., Jabado, N., & Lewis, P. W. (2019). PFA ependymoma-associated protein EZHIP inhibits PRC2 activity through a H3 K27M-like mechanism. Nat Commun, 10(1), 2146. https://doi.org/10.1038/s41467-019-09981-6.
Jubierre, L., Jimenez, C., Rovira, E., Soriano, A., Sabado, C., Gros, L., Llort, A., Hladun, R., Roma, J., Toledo, J. S., Gallego, S., & Segura, M. F. (2018). Targeting of epigenetic regulators in neuroblastoma. Exp Mol Med, 50(4), 1-12. https://doi.org/10.1038/s12276-018-0077-2.
Krug, B., De Jay, N., Harutyunyan, A. S., Deshmukh, S., Marchione, D. M., Guilhamon, P., Bertrand, K. C., Mikael, L. G., McConechy, M. K., Chen, C. C. L., Khazaei, S., Koncar, R. F., Agnihotri, S., Faury, D., Ellezam, B., Weil, A. G., Ursini-Siegel, J., De Carvalho, D. D., Dirks, P. B., . . . Mack, S. C. (2019). Pervasive H3K27 Acetylation Leads to ERV Expression and a Therapeutic Vulnerability in H3K27M Gliomas. Cancer Cell, 35(5), 782-797 e788. https://doi.org/10.1016/j.ccell.2019.04.004.
Lapin, D. H., Tsoli, M., & Ziegler, D. S. (2017). Genomic Insights into Diffuse Intrinsic Pontine Glioma. Front Oncol, 7, 57. https://doi.org/10.3389/fonc.2017.00057.
Li, W. C., Xiong, Z. Y., Huang, P. Z., Liao, Y. J., Li, Q. X., Yao, Z. C., Liao, Y. D., Xu, S. L., Zhou, H., Wang, Q. L., Huang, H., Zhang, P., Lin, J. Z., Liu, B., Ren, J., & Hu, K. P. (2019). KCNK levels are prognostic and diagnostic markers for hepatocellular carcinoma. Aging (Albany NY), 11(19), 8169-8182. https://doi.org/10.18632/aging.102311.
Lin, G. L., Wilson, K. M., Ceribelli, M., Stanton, B. Z., Woo, P. J., Kreimer, S., Qin, E. Y., Zhang, X., Lennon, J., Nagaraja, S., Morris, P. J., Quezada, M., Gillespie, S. M., Duveau, D. Y., Michalowski, A. M., Shinn, P., Guha, R., Ferrer, M., Klumpp-Thomas, C., . . . Monje, M. (2019). Therapeutic strategies for diffuse midline glioma from high-throughput combination drug screening. Sci Transl Med, 11(519). https://doi.org/10.1126/scitranslmed.aaw0064.
Liu, R., Shuai, Y., Luo, J., & Zhang, Z. (2019). SEMA3C Promotes Cervical Cancer Growth and Is Associated With Poor Prognosis. Front Oncol, 9, 1035. https://doi.org/10.3389/fonc.2019.01035.
Long, T., Hassan, A., Thompson, B. M., McDonald, J. G., Wang, J., & Li, X. (2019). Structural basis for human sterol isomerase in cholesterol biosynthesis and multidrug recognition. Nat Commun, 10(1), 2452. https://doi.org/10.1038/s41467-019-10279-w.
Mazzio, E. A., & Soliman, K. F. A. (2018). Whole-transcriptomic Profile of SK-MEL-3 Melanoma Cells Treated with the Histone Deacetylase Inhibitor: Trichostatin A. Cancer Genomics Proteomics, 15(5), 349-364. https://doi.org/10.21873/cgp.20094.
Nagaraja, S., Vitanza, N. A., Woo, P. J., Taylor, K. R., Liu, F., Zhang, L., Li, M., Meng, W., Ponnuswami, A., Sun, W., Ma, J., Hulleman, E., Swigut, T., Wysocka, J., Tang, Y., & Monje, M. (2017). Transcriptional Dependencies in Diffuse Intrinsic Pontine Glioma. Cancer Cell, 31(5), 635-652 e636. https://doi.org/10.1016/j.ccell.2017.03.011.
Park, A., & Harris, L. K. (2021). Gene Expression Meta-Analysis Reveals Interferon-Induced Genes Associated With SARS Infection in Lungs. Front Immunol, 12, 694355. https://doi.org/10.3389/fimmu.2021.694355.
Peacock, J. W., Takeuchi, A., Hayashi, N., Liu, L., Tam, K. J., Al Nakouzi, N., Khazamipour, N., Tombe, T., Dejima, T., Lee, K. C., Shiota, M., Thaper, D., Lee, W. C., Hui, D. H., Kuruma, H., Ivanova, L., Yenki, P., Jiao, I. Z., Khosravi, S., . . . Ong, C. J. (2018). SEMA3C drives cancer growth by transactivating multiple receptor tyrosine kinases via Plexin B1. EMBO Mol Med, 10(2), 219-238. https://doi.org/10.15252/emmm.201707689.
Pellot, J. E., & De Jesus, O. (2021). Diffuse Intrinsic Pontine Glioma. StatPearls [Internet].
Rechberger, J. S., Lu, V. M., Zhang, L., Power, E. A., & Daniels, D. J. (2020). Clinical trials for diffuse intrinsic pontine glioma: the current state of affairs. Childs Nerv Syst, 36(1), 39-46. https://doi.org/10.1007/s00381-019-04363-1.
Sahni, J. M., & Keri, R. A. (2018). Targeting bromodomain and extraterminal proteins in breast cancer. Pharmacol Res, 129, 156-176. https://doi.org/10.1016/j.phrs.2017.11.015.
Schinke, C. D., Bird, J. T., Qu, P., Yaccoby, S., Lyzogubov, V. V., Shelton, R., Ling, W., Boyle, E. M., Deshpande, S., Byrum, S. D., Washam, C., Mackintosh, S., Stephens, O., Thanendrarajan, S., Zangari, M., Shaughnessy, J., Jr., Zhan, F., Barlogie, B., van Rhee, F., & Walker, B. A. (2021). PHF19 inhibition as a therapeutic target in multiple myeloma. Curr Res Transl Med, 69(3), 103290. https://doi.org/10.1016/j.retram.2021.103290.
Srikanthan, D., Taccone, M. S., Van Ommeren, R., Ishida, J., Krumholtz, S. L., & Rutka, J. T. (2021). Diffuse intrinsic pontine glioma: current insights and future directions. Chin Neurosurg J, 7(1), 6. https://doi.org/10.1186/s41016-020-00218-w.
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., & Mesirov, J. P. (2005). Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A, 102(43), 15545-15550. https://doi.org/10.1073/pnas.0506580102.
Taylor, I. C., Hutt-Cabezas, M., Brandt, W. D., Kambhampati, M., Nazarian, J., Chang, H. T., Warren, K. E., Eberhart, C. G., & Raabe, E. H. (2015). Disrupting NOTCH Slows Diffuse Intrinsic Pontine Glioma Growth, Enhances Radiation Sensitivity, and Shows Combinatorial Efficacy With Bromodomain Inhibition. J Neuropathol Exp Neurol, 74(8), 778-790. https://doi.org/10.1097/NEN.0000000000000216.
Theodoropoulos, P. C., Wang, W., Budhipramono, A., Thompson, B. M., Madhusudhan, N., Mitsche, M. A., McDonald, J. G., De Brabander, J. K., & Nijhawan, D. (2020). A Medicinal Chemistry-Driven Approach Identified the Sterol Isomerase EBP as the Molecular Target of TASIN Colorectal Cancer Toxins. J Am Chem Soc, 142(13), 6128-6138. https://doi.org/10.1021/jacs.9b13407.
Tu, B., Zhang, M., Liu, T., & Huang, Y. (2020). Nanotechnology-Based Histone Deacetylase Inhibitors for Cancer Therapy. Front Cell Dev Biol, 8, 400. https://doi.org/10.3389/fcell.2020.00400.
Wang, J., Huang, T. Y., Hou, Y., Bartom, E., Lu, X., Shilatifard, A., Yue, F., & Saratsis, A. (2021). Epigenomic landscape and 3D genome structure in pediatric high-grade glioma. Sci Adv, 7(23). https://doi.org/10.1126/sciadv.abg4126.
Wang, L., Tan, T. K., Durbin, A. D., Zimmerman, M. W., Abraham, B. J., Tan, S. H., Ngoc, P. C. T., Weichert-Leahey, N., Akahane, K., Lawton, L. N., Rokita, J. L., Maris, J. M., Young, R. A., Look, A. T., & Sanda, T. (2019). ASCL1 is a MYCN- and LMO1-dependent member of the adrenergic neuroblastoma core regulatory circuitry. Nat Commun, 10(1), 5622. https://doi.org/10.1038/s41467-019-13515-5.
Wang, S. C., Liao, L. M., Ansar, M., Lin, S. Y., Hsu, W. W., Su, C. M., Chung, Y. M., Liu, C. C., Hung, C. S., & Lin, R. K. (2021). Automatic Detection of the Circulating Cell-Free Methylated DNA Pattern of GCM2, ITPRIPL1 and CCDC181 for Detection of Early Breast Cancer and Surgical Treatment Response. Cancers (Basel), 13(6). https://doi.org/10.3390/cancers13061375.
Dr. Laura K. Harris
Institute for Cyber Enabled Research, Michigan State University, East Lansing, 48824 - United States of America