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

作　　者：Zhongyao Chen Qiang Gao Yukui Shang Behzad Nasiri Ahmadabadi Yawei Hu Wei Zhang Peng Liu 

机构地区：[1]Department of Biomedical Engineering,School of Medicine,Tsinghua University,Beijing,China [2]School of Clinical Medicine,Tsinghua University,Beijing,China [3]IDG/McGovern Institute for Brain Research,School of Life Sciences,Tsinghua University,Beijing,China [4]Department of Basic Medical Sciences,School of Medicine,Tsinghua University,Beijing,China [5]Department of Paediatrics,Faculty of Medicine,CUHK–Hub of Paediatric Excellence,The Chinese University of Hong Kong,Hong Kong,China [6]Changping National Laboratory,Beijing,China [7]Department of Neurosurgery,Beijing Tsinghua Changgung Hospital,Tsinghua University,Beijing,China [8]Department of Neurosurgery,Beijing Children’s Hospital,Capital Medical University,National Center for Children’s Health,Beijing,China

出　　处：《hLife》2024年第9期471-487,共17页健康科学（英文）

基　　金：supported by grants from the National Science Foundation of China(No.22127804);the National Natural Science Foundation of China(No.81771931 and 31971325);Institute of Biomedicine,the Tsinghua-Peking Joint Center for Life Sciences,and the Clinical Medicine Development Fund of Tsinghua University(No.10001020510);the National Key Research and Development Program of China(No.2016YFC0900200).

摘　　要：Diffuse midline glioma(DMG),H3K27-altered,is lethal pediatric-type,high-grade,localized to the midline region of the central nervous system.Effective treatment guidelines are absent,and clinical trials are preferred for primary or recur-rent DMG patients.Recently,epigenetic agent-based immunotherapy has exhibited promising therapeutic effects in the clinical setting.However,the underlying mechanisms remain a mystery.The rare DMG tumor samples from biopsy or resection largely impede basic research,by using patient-derived tumor cells which better recapitulate the parental tu-mor’s heterogeneity compared to established cell lines.As an epigenetic reprogramming disease,DMG exhibits a global loss of H3K27 trimethylation(H3K27me3)and a gain of H3K27 acetylation(H3K27ac).Analysis of multiple epige-netic marks is fundamentally necessary.However,traditional techniques cannot allow ultra-low input and high-throughput.Herein we have developed a new method called high-throughput in situ tagged immunoprecipitation sequencing(HiTIP-seq),which uses an integrated superhydrophobic microwell array technology(InSMART).We were able to perform 100 parallel assays from as few as 100 cells per microwell on a single chip.We applied the tech-nology to profile epigenetic alterations of three-dimensional(3D)cell cultures derived from DMG patients.Our HiTIP-seq integrated with RNA sequencing(RNA-seq)analysis revealed that the combination of epigenetic agents(panobino-stat and tazemetostat),reprogrammed histone modifications and drove transcriptome changes.Among them,Wnt inhibitory factor 1(WIF1)has a gain of H3K27ac and a loss of H3K27me3,which leads to the upregulated expression.Altogether,HiTIP-seq is a versatile method for high-throughput analysis of histone modifications,suitable for both DMG research and studying rare 3D models.

关 键 词：diffuse midline glioma high-throughput chromatin immunoprecipitation sequencing(ChIP-seq) epigenetic therapy histone modification 

分 类 号：R739.41[医药卫生—肿瘤]