HiTIP-seq profiles epigenomic reprogramming of patient-derived diffuse midline glioma stem cells to epigenetic therapy

News Release 24-Sep-2024

Peer-Reviewed Publication
Tsinghua University Press

image:

Diffuse midline glioma (DMG), H3K27-altered, is a lethal pediatric high-grade tumor, lacking effective treatment options, primarily depending on clinical trials. Epigenetic agent-based immunotherapy has shown promise, but the underlying mechanisms remain unclear. To address the scarcity of tumor samples, researchers utilize patient-derived tumor cells to explore DMG heterogeneity. The epigenetic characteristics of DMG include a loss of H3K27me3 and a gain of H3K27ac. To overcome the limitations of traditional techniques, we developed high-throughput in situ tagged immunoprecipitation sequencing (HiTIP-seq) utilizing InSMART, enabling 100 parallel assays from just 100 cells on a single chip. Using this new method, we analyzed epigenetic alterations in 3D cell cultures derived from DMG patients, discovering that combinations of epigenetic agents (such as panobinostat and tazemetostat) can reprogram histone modifications and drive transcriptome changes, notably upregulating WIF1. HiTIP-seq provides a new tool for DMG research, showcasing hope in the fight against this deadly disease, and may ultimately lead to effective treatment options in the future.

Credit: Peng Liu, School of Biomedical Engineering, Tsinghua University

Diffuse midline glioma (DMG) is a highly aggressive and fatal pediatric high-grade glioma that primarily affects critical regions of the central nervous system, such as the pons, thalamus, and spinal cord. Due to the high surgical risks and poor prognosis associated with DMG, treatment options for patients are extremely limited. Conventional treatments, including surgery, radiotherapy, and chemotherapy, have shown limited efficacy, particularly with radiochemotherapy, which only temporarily controls tumor progression without significantly extending patient survival. Most patients succumb to the disease within two years of diagnosis, and effective therapeutic strategies are currently lacking.

One of the key pathological features of DMG is the lysine-to-methionine mutation at position 27 of histone H3 (H3K27M), which disrupts the epigenomic regulation of cells and drives rapid cancer progression. Studies have shown that epigenetic therapies can reprogram histone modifications in DMG tumor cells, thereby suppressing the expression of genes associated with tumor progression. However, the scarcity of DMG samples and the complexity of culturing tumor cells have hindered progress in both research and treatment.

In response, the researchers developed HiTIP-seq, a microarray-based high-throughput in situ tagged immunoprecipitation sequencing technology. Compared to traditional chromatin immunoprecipitation sequencing (ChIP-seq), HiTIP-seq enables high-throughput retrieval of high-quality epigenomic modification information from limited cell samples, providing new strategies for studying diseases like DMG that rely on scarce sample sources.

The study demonstrates that the combination of epigenetic drugs Panobinostat and Tazemetostat can reprogram histone modifications in tumor cells, thereby suppressing the expression of genes associated with cancer progression. Using HiTIP-seq, the researchers conducted an in-depth analysis of epigenetic modifications in 3D cell cultures derived from DMG patients, revealing that these drugs effectively inhibit tumor cell growth by increasing H3K27 acetylation (H3K27ac) and decreasing H3K27 trimethylation (H3K27me3).

Furthermore, integrative transcriptomic analysis (RNA-seq) showed that the combination therapy activates the Wnt signaling pathway inhibitory factor 1 (WIF1), thereby inhibiting tumor cell proliferation and dissemination. This discovery not only highlights the potential sensitivity of DMG to epigenetic therapy but also provides critical scientific insights for future DMG treatment strategies.

In conclusion, the HiTIP-seq platform enables the acquisition of high-quality epigenomic modification information from limited sample sizes. Coupled with high-throughput microarray technology, this approach allows for simultaneous analysis of multiple samples and drug combinations. This innovation paves the way for novel research and therapeutic strategies targeting diffuse midline glioma (DMG), offering new hope for patients. Moreover, HiTIP-seq provides a powerful tool for advancing epigenetic research in other cancers, driving significant progress in the field of cancer therapeutics.

Journal
hLife

DOI
10.1016/j.hlife.2024.07.004

Article Title
HiTIP-seq profiles epigenomic reprogramming of patient-derived diffuse midline glioma stem cells to epigenetic therapy

Article Publication Date
23-Sep-2024