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Kim HS, Kim YI, Cho JY. ARID3C Acts as a Regulator of Monocyte-to-Macrophage Differentiation Interacting with NPM1. J Proteome Res 2024; 23:2882-2892. [PMID: 38231884 PMCID: PMC11302414 DOI: 10.1021/acs.jproteome.3c00509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/19/2024]
Abstract
ARID3C is a protein located on human chromosome 9 and expressed at low levels in various organs, yet its biological function has not been elucidated. In this study, we investigated both the cellular localization and function of ARID3C. Employing a combination of LC-MS/MS and deep learning techniques, we identified NPM1 as a binding partner for ARID3C's nuclear shuttling. ARID3C was found to predominantly localize with the nucleus, where it functioned as a transcription factor for genes STAT3, STAT1, and JUNB, thereby facilitating monocyte-to-macrophage differentiation. The precise binding sites between ARID3C and NPM1 were predicted by AlphaFold2. Mutating this binding site prevented ARID3C from interacting with NPM1, resulting in its retention in the cytoplasm instead of translocation to the nucleus. Consequently, ARID3C lost its ability to bind to the promoters of target genes, leading to a loss of monocyte-to-macrophage differentiation. Collectively, our findings indicate that ARID3C forms a complex with NPM1 to translocate to the nucleus, acting as a transcription factor that promotes the expression of the genes involved in monocyte-to-macrophage differentiation.
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Affiliation(s)
- Hui-Su Kim
- Department
of Biochemistry, College of Veterinary Medicine, Research Institute
for Veterinary Science, and BK21 FOUR Future Veterinary Medicine Leading
Education and Research Center, Seoul National
University, Seoul 08826, Republic of Korea
- Comparative
Medicine Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul 08826, Republic of Korea
| | - Yong-In Kim
- Department
of Biochemistry, College of Veterinary Medicine, Research Institute
for Veterinary Science, and BK21 FOUR Future Veterinary Medicine Leading
Education and Research Center, Seoul National
University, Seoul 08826, Republic of Korea
- Comparative
Medicine Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul 08826, Republic of Korea
| | - Je-Yoel Cho
- Department
of Biochemistry, College of Veterinary Medicine, Research Institute
for Veterinary Science, and BK21 FOUR Future Veterinary Medicine Leading
Education and Research Center, Seoul National
University, Seoul 08826, Republic of Korea
- Comparative
Medicine Disease Research Center (CDRC), Science Research Center (SRC), Seoul National University, Seoul 08826, Republic of Korea
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2
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Mao X, Xu J, Xiao M, Liang C, Hua J, Liu J, Wang W, Yu X, Meng Q, Shi S. ARID3A enhances chemoresistance of pancreatic cancer via inhibiting PTEN-induced ferroptosis. Redox Biol 2024; 73:103200. [PMID: 38781729 PMCID: PMC11145557 DOI: 10.1016/j.redox.2024.103200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 05/03/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024] Open
Abstract
Currently, chemotherapy remains occupying a pivotal place in the treatment of pancreatic ductal adenocarcinoma (PDAC). Nonetheless, the emergence of drug resistance in recent years has limited the clinical efficacy of chemotherapeutic agents, especially gemcitabine (GEM). Through bioinformatics analysis, AT-rich Interactive Domain-containing Protein 3A (ARID3A), one of transcription factors, is discovered to possibly participate in this progress. This study thoroughly investigates the potential role of ARID3A in the malignant progression and GEM chemoresistance of PDAC and explores the underlying mechanisms. The results indicate that ARID3A knockdown suppresses tumor development and enhances the sensitivity of PDAC cells to GEM in vitro and vivo. Mechanically, CUT&Tag profiling sequencing, RNA-sequencing and functional studies demonstrates that decreased ARID3A expression alleviates the transcriptional inhibition of phosphatase and tensin homolog (PTEN), consequently leading to glutathione peroxidase 4 (GPX4) depletion and increased lipid peroxidation levels. Activated ferroptosis induced by the inhibition of GPX4 subsequently restricts tumor progression and reduces GEM resistance in PDAC. This research identifies the ferroptosis regulatory pathway of ARID3A-PTEN-GPX4 axis and reveals its critical role in driving the progression and chemoresistance of pancreatic cancer. Notably, both inhibition of ARID3A and enhancement of ferroptosis can increase chemosensitivity to GEM, which offers a promising opportunity for developing therapeutic strategies to combat acquired chemotherapy resistance in pancreatic cancer.
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Affiliation(s)
- Xiaoqi Mao
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai, 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, China
| | - Jin Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai, 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, China
| | - Mingming Xiao
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai, 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, China
| | - Chen Liang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai, 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, China
| | - Jie Hua
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai, 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, China
| | - Jiang Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai, 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, China
| | - Wei Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai, 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai, 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, China.
| | - Qingcai Meng
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai, 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, China.
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, 200032, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032, China; Shanghai Pancreatic Cancer Institute, Shanghai, 200032, China; Pancreatic Cancer Institute, Fudan University, Shanghai, 200032, China.
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3
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Nasuh S, Balci SO, Bozgeyik I, Ikeda MA, Tekayev M, Saadat KASM. ARID3A and ARID3B exert direct regulatory control over the long non-coding RNAs (lncRNAs) MALAT1 and NORAD within the context of non-small cell lung cancer (NSCLC). Pathol Res Pract 2023; 252:154948. [PMID: 37977034 DOI: 10.1016/j.prp.2023.154948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/10/2023] [Indexed: 11/19/2023]
Abstract
Lung cancer, known for its high mortality rates and poor prognosis, remains one of the most prevalent cancer types. Early detection and effective treatment methods are crucial for improving survival rates. Non-small cell lung cancer (NSCLC) accounts for approximately 85 % of all lung cancer cases. Long non-coding RNAs (lncRNAs), which play vital roles in various biological processes, have been implicated in the development of cancer and can impact key therapeutic targets in different cancer types. In NSCLC, the dysregulation of specific lncRNAs, such as MALAT1 and NORAD, has been associated with neoplastic initiation, progression, metastasis, tumor angiogenesis, chemoresistance, and genomic instability. Both MALAT1 and NORAD directly regulate the expression of the transcription factor E2F1, thereby influencing cell cycle progression. Additionally, MALAT1 has been reported to affect the expression of p53 target genes, leading to cell cycle progression through the repression of p53 promoter activity. NORAD, on the other hand, is indirectly regulated by p53. The AT-rich interaction domain (ARID) family of DNA-binding proteins, particularly ARID3A and ARID3B, are involved in various biological processes such as cell proliferation, differentiation, and development. They also play significant roles in E2F-dependent transcription and are transcriptional targets of p53. The intricate balance between promoting cellular proliferation through the pRB-E2F pathway and inducing growth arrest through the p53 pathway underscores the crucial regulatory role of ARID3A, ARID3B, and their interaction with lncRNAs MALAT1 and NORAD. In this study, we aimed to investigate the potential interactive and functional connections among ARID3A, ARID3B, MALAT1, and NORAD in NSCLC, considering their involvement in the pRB-E2F and p53 pathways. Our findings strongly suggest that ARID3A and ARID3B play a regulatory role in controlling MALAT1 and NORAD in NSCLC. Specifically, our study demonstrates that the activities of MALAT1 and NORAD were markedly increased upon the overexpression of ARID3A and ARID3B. Therefore, we can conclude that ARID3A and ARID3B likely contribute significantly to the oncogenic functions of MALAT1 and NORAD in NSCLC. Consequently, targeting ARID3A and ARID3B could hold promise as a therapeutic approach in NSCLC, given their direct control over the expression of MALAT1 and NORAD.
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Affiliation(s)
- Sedin Nasuh
- Department of Medical Biology and Genetics, Faculty of Medicine, Graduate Institute of Health Sciences, Gaziantep University, Gaziantep 27310, Turkey
| | - Sibel Oguzkan Balci
- Department of Medical Biology and Genetics, Faculty of Medicine, Graduate Institute of Health Sciences, Gaziantep University, Gaziantep 27310, Turkey
| | - Ibrahim Bozgeyik
- Department of Medical Biology, Faculty of Medicine Adiyaman University, Adiyaman 02040, Turkey
| | - Masa-Aki Ikeda
- Department of Regenerative and Reconstructive Dental Medicine, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan; Department of Molecular Craniofacial Embryology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Muhammetnur Tekayev
- Department of Medical Biology and Genetics, Faculty of Medicine, Graduate Institute of Health Sciences, Gaziantep University, Gaziantep 27310, Turkey; Department of Histology and Embryology, Hamidiye Faculty of Medicine, Hamidiye Institute of Health Sciences, University of Health Sciences, Istanbul 34668, Turkey
| | - Khandakar A S M Saadat
- Department of Medical Biology and Genetics, Faculty of Medicine, Graduate Institute of Health Sciences, Gaziantep University, Gaziantep 27310, Turkey.
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4
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Jackson C, Cherry C, Bom S, Dykema AG, Thompson E, Zheng M, Ji Z, Hou W, Li R, Zhang H, Choi J, Rodriguez F, Weingart J, Yegnasubramanian S, Lim M, Bettegowda C, Powell J, Eliesseff J, Ji H, Pardoll D. Distinct Myeloid Derived Suppressor Cell Populations Promote Tumor Aggression in Glioblastoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.26.534192. [PMID: 37034584 PMCID: PMC10081225 DOI: 10.1101/2023.03.26.534192] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The diversity of genetic programs and cellular plasticity of glioma-associated myeloid cells, and thus their contribution to tumor growth and immune evasion, is poorly understood. We performed single cell RNA-sequencing of immune and tumor cells from 33 glioma patients of varying tumor grades. We identified two populations characteristic of myeloid derived suppressor cells (MDSC), unique to glioblastoma (GBM) and absent in grades II and III tumors: i) an early progenitor population (E-MDSC) characterized by strong upregulation of multiple catabolic, anabolic, oxidative stress, and hypoxia pathways typically observed within tumor cells themselves, and ii) a monocytic MDSC (M-MDSC) population. The E-MDSCs geographically co-localize with a subset of highly metabolic glioma stem-like tumor cells with a mesenchymal program in the pseudopalisading region, a pathognomonic feature of GBMs associated with poor prognosis. Ligand-receptor interaction analysis revealed symbiotic cross-talk between the stemlike tumor cells and E-MDSCs in GBM, whereby glioma stem cells produce chemokines attracting E-MDSCs, which in turn produce growth and survival factors for the tumor cells. Our large-scale single-cell analysis elucidated unique MDSC populations as key facilitators of GBM progression and mediators of tumor immunosuppression, suggesting that targeting these specific myeloid compartments, including their metabolic programs, may be a promising therapeutic intervention in this deadly cancer. One-Sentence Summary Aggressive glioblastoma harbors two unique myeloid populations capable of promoting stem-like properties of tumor cells and suppressing T cell function in the tumor microenvironment.
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5
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Guo X, Qi H, Lin G, Yu J, Zhang M, Gao X. ARID3A plays a key regulatory role in palmitic acid-stimulated milk fat synthesis in mouse mammary epithelial cells. Cell Biol Int 2023; 47:1106-1117. [PMID: 36786478 DOI: 10.1002/cbin.12003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 01/18/2023] [Accepted: 02/05/2023] [Indexed: 02/15/2023]
Abstract
Palmitic acid (PA) can stimulate milk fat synthesis in mammary gland, but the specific mechanism is still unclear. In our research, we aim to explore the role and corresponding mechanism of AT-rich interaction domain 3A (ARID3A) in milk fat synthesis stimulated by PA. We found that ARID3A protein level in mouse mammary gland tissues during lactation was much higher than that during puberty and involution. ARID3A knockdown and gene activation showed that ARID3A stimulated the synthesis of triglycerides and cholesterol in HC11 cells, secretion of free fatty acids from cells and lipid droplet formation in cells. ARID3A also promoted the expression and maturation of SREBP1 in HC11 cells. PA stimulated ARID3A protein expression and SREBP1 expression and maturation in a dose-dependent manner, and the PI3K specific inhibitor LY294002 blocked the stimulation of PA on ARID3A expression. ARID3A knockdown blocked the stimulation of PA on SREBP1 protein expression and maturation. We further showed that ARID3A was localized in the nucleus and PA stimulated this localization, and ARID3A knockdown blocked the stimulation of PA on the mRNA expression of SREBP1. To sum up, our data reveal that ARID3A is a key mediator for PA to promote SREBP1 mRNA expression and stimulate milk fat synthesis in mammary epithelial cells.
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Affiliation(s)
- Xudong Guo
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Hao Qi
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Gang Lin
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Jiaxiao Yu
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Minghui Zhang
- College of Animal Science, Yangtze University, Jingzhou, China
| | - Xuejun Gao
- College of Animal Science, Yangtze University, Jingzhou, China
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6
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Zhang X, Qiu X, Zhao W, Song L, Zhang X, Yang L, Tao M. Over-Expression of ARID3B Suppresses Tumor Progression and Predicts Better Prognosis in Patients With Gastric Cancer. Cancer Control 2023; 30:10732748231169403. [PMID: 37071790 PMCID: PMC10126794 DOI: 10.1177/10732748231169403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2023] Open
Abstract
BACKGROUND ARID3B (AT-rich interaction domain 3B) has been demonstrated to be associated with the progression and patient prognosis of several human tumors. We conducted the present study to investigate the biological behavior and clinical relevance of ARID3B in gastric cancer (GC). METHODS Detection of the expression level in GC tissues and cell lines were performed by Western blot and immunohistochemistry. We also retrospectively analyzed the correlation of ARID3B with clinicopathological characteristics and patient prognosis in gastric cancer. The biological functions of ARID3B in GC cells were further explored by transwell migration assays, wound healing assays and cell proliferation assay. RESULTS The present study suggested that the expression of ARID3B was significantly lower in GC tissues than in adjacent normal tissues. IHC staining in tissues of 406 GC patients from training and validation sets verified that ARID3B over-expression correlated with clinicopathological features, such as degree of differentiation and clinical stage. Meanwhile, ARID3B was proved to be an independent prognostic factor for GC prognosis. Furthermore, over-expression of ARID3B suppressed proliferation in GC cells according CCK8 assay. We found that over-expression of ARID3B inhibited GC cell migration by transwell assay and wound healing assay. Furthermore, EMT markers were detected in ARID3B over-expression GC cells, which showed that ARID3B may inhibit metastasis of GC cells. CONCLUSION Our results firstly revealed that the expression level of ARID3B was closely correlated with clinicopathological features and may serve as an independent prognostic factor for GC patients. More importantly, ARID3B could suppress GC progression, including cell proliferation, migration and metastasis.
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Affiliation(s)
- Xunlei Zhang
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xinyue Qiu
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Wenjing Zhao
- Cancer Research Center, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Li Song
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Xingsong Zhang
- Department of Pathology, Affiliated Tumor Hospital of Nantong University, Nantong Jiangsu, China
| | - Lei Yang
- Department of Oncology, Affiliated Tumor Hospital of Nantong University, Nantong, Jiangsu, China
| | - Min Tao
- Department of Oncology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
- Department of Oncology, Dushu Lake Hospital Affiliated to Soochow University, Suzhou, Jiangsu, China
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7
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Shen M, Li S, Zhao Y, Liu Y, Liu Z, Huan L, Qiao Y, Wang L, Han L, Chen Z, He X. Hepatic ARID3A facilitates liver cancer malignancy by cooperating with CEP131 to regulate an embryonic stem cell-like gene signature. Cell Death Dis 2022; 13:732. [PMID: 36008383 PMCID: PMC9411159 DOI: 10.1038/s41419-022-05187-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 08/10/2022] [Accepted: 08/12/2022] [Indexed: 01/21/2023]
Abstract
Liver cancer stemness refers to the stem cell-like phenotype of hepatocarcinoma cells and is closely related to a high degree of tumour malignancy. Here, we identified AT-rich interacting domain 3A (ARID3A) as one of the most upregulated stemness-related transcription factors in liver cancer by an in vitro functional screen. ARID3A can promote liver cancer cell viability and metastasis both in vitro and in vivo. Mechanistically, ARID3A interacts with CEP131 and transcriptionally activates KDM3A by co-occupying its promoter element, further upregulating the expression of downstream embryonic stem (ES) signature genes via demethylation of H3K9me2. ARID3A and CEP131 promote an ES cell gene signature through activation of KDM3A and contribute to the poor prognosis of liver cancer patients. Collectively, these results provide evidence highlighting a transcription-dependent mechanism of ARID3A in stemness regulation in liver cancer. The ARID3A/CEP131-KDM3A regulatory circuit could serve as a prognostic indicator and potential therapeutic target for liver cancer.
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Affiliation(s)
- Mengting Shen
- grid.8547.e0000 0001 0125 2443Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Shengli Li
- grid.16821.3c0000 0004 0368 8293Precision Research Center for Refractory Diseases, Institute for Clinical Research, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201620 China
| | - Yiming Zhao
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
| | - Yizhe Liu
- grid.8547.e0000 0001 0125 2443Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Zhen Liu
- grid.8547.e0000 0001 0125 2443Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Lin Huan
- grid.8547.e0000 0001 0125 2443Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Yejun Qiao
- grid.8547.e0000 0001 0125 2443Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Lu Wang
- Department of Hepatic Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
| | - Leng Han
- grid.264756.40000 0004 4687 2082Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, Texas A&M University, Houston, TX 77030 USA
| | - Zhiao Chen
- grid.8547.e0000 0001 0125 2443Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032 China ,Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
| | - Xianghuo He
- grid.8547.e0000 0001 0125 2443Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, 200032 China ,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032 China ,Shanghai Key Laboratory of Radiation Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032 China
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8
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The Prognostic Value of AT-Rich Interaction Domain (ARID) Family Members in Patients with Hepatocellular Carcinoma. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:1150390. [PMID: 36034939 PMCID: PMC9410793 DOI: 10.1155/2022/1150390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 07/19/2022] [Indexed: 12/24/2022]
Abstract
Objective Hepatocellular carcinoma (HCC) is one of the most lethal malignancies with a poor prognosis. The AT-rich interaction domain (ARID) family plays an essential regulatory role in the pathogenesis and progression of cancers. This study aims to evaluate the prognostic value and clinical significance of human ARID family genes in HCC. Methods ONCOMINE and The Cancer Genome Atlas (TCGA) databases were employed to retrieve ARIDs expression profile and clinicopathological information of HCC. Kaplan–Meier plotter and MethSurv were applied to the survival analysis of patients with HCC. CBioPortal was used to analyze genetic mutations of ARIDs. Gene Expression Profiling Interactive Analysis (GEPIA) and Metascape were used to perform hub gene identification and functional enrichment. Results Expression levels of 11 ARIDs were upregulated in HCC, and 2 ARIDs were downregulated. Also, 4 ARIDs and 5 ARIDs were correlated with pathologic stages and histologic grades, respectively. Furthermore, higher expression of ARID1A, ARID1B, ARID2, ARID3A, ARID3B, ARID5B, KDM5A, KDM5B, KDM5C, and JARID2 was remarkably correlated with worse overall survival of patients with HCC, and the high ARID3C/KDM5D expression was related to longer overall survival. Multivariate Cox analysis indicated that ARID3A, KDM5C, and KDM5D were independent risk factors for HCC prognosis. Moreover, ARIDs mutations and 127 CpGs methylation in all ARIDs were observed to be significantly associated with the prognosis of HCC patients. Besides, our data showed that ARIDs could regulate tumor-related pathways and distinct immune cells in the HCC microenvironment. Conclusions ARIDs present the potential prognostic value for HCC. Our findings suggest that ARID3A, KDM5C, and KDM5D may be the prognostic biomarkers for patients with HCC.
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9
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Li Y, Tang J, Li J, Du Y, Bai F, Yang L, Li X, Jin X, Wang T. ARID3A promotes the chemosensitivity of colon cancer by inhibiting AKR1C3. Cell Biol Int 2022; 46:965-975. [PMID: 35257428 DOI: 10.1002/cbin.11789] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 02/02/2022] [Accepted: 02/25/2022] [Indexed: 11/09/2022]
Abstract
ARID3A is upregulated in colorectal cancer and can promote the proliferation and metastasis of cancer cells. However, patients with higher level of ARID3A have a better prognosis. This study aimed to uncover the mechanism by which ARID3A benefits the prognosis of colon cancer. Our results indicated that ARID3A upregulation enhanced the chemosensitivity of colon cancer cells to 5-Fluorouracil (5-FU), whereas ARID3A downregulation inhibited the chemosensitivity of colon cancer cells to 5-FU. Through database analysis, we found that AKR1C3, a drug resistance related gene, was the target of ARID3A. Moreover, AKR1C3 was downregulated in colon cancer tissues compared to normal tissues. Next, we assessed the interaction between AKR1C3 and ARID3A, and found that ARID3A inhibited the transcription of AKR1C3, leading to the downregulation of AKR1C3 in colon cancer cells. We also verified that AKR1C3 inhibited the chemosensitivity of colon cancer cells to 5-FU. Moreover, patients with higher ratio of ARID3A to AKR1C3 had a better prognosis. This study suggested that ARID3A promoted chemosensitivity of colon cancer cells by inhibiting AKR1C3 in colon cancer. The ratio of ARID3A to AKR1C3 is a good marker to predict the prognosis of colon cancer patients. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yafei Li
- Department of Pathology, Harbin Medical University, Harbin, 150081, China
| | - Jing Tang
- Department of Pathology, Harbin Medical University, Harbin, 150081, China
| | - Jing Li
- Department of Pathology, Harbin Medical University, Harbin, 150081, China
| | - Yaru Du
- Department of Pathology, Harbin Medical University, Harbin, 150081, China
| | - Fuqiang Bai
- Department of Pathology, Harbin Medical University, Harbin, 150081, China
| | - Lirui Yang
- Department of Pathology, Harbin Medical University, Harbin, 150081, China
| | - Xiaobo Li
- Department of Pathology, Harbin Medical University, Harbin, 150081, China
| | - Xiaoming Jin
- Department of Pathology, Harbin Medical University, Harbin, 150081, China
| | - Tianzhen Wang
- Department of Pathology, Harbin Medical University, Harbin, 150081, China
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10
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Zheng W, Lai G, Lin Q, Issah MA, Fu H, Shen J. A miR-129-5P/ARID3A Negative Feedback Loop Modulates Diffuse Large B Cell Lymphoma Progression and Immune Evasion Through Regulating the PD-1/PD-L1 Checkpoint. Front Cell Dev Biol 2021; 9:735855. [PMID: 34778251 PMCID: PMC8579866 DOI: 10.3389/fcell.2021.735855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 10/05/2021] [Indexed: 12/14/2022] Open
Abstract
The activated B cell (ABC) and germinal center B cell (GCB) subtypes of diffuse large B cell lymphoma (DLBCL) have different gene expression profiles and clinical outcomes, and miRNAs have been reported to play important roles in tumorigenesis, progression, and metastasis. This study aimed to explore the differentially expressed miRNAs and target genes in the two main subtypes of DLBCL. Hub miRNAs were identified by constructing a regulatory network, and in vitro experiments and peripheral blood samples of DLBCL were used to explore the functions and mechanisms of differential miRNAs and mRNAs. Differentially expressed miRNAs and genes associated with the two DLBCL subtypes were identified using GEO datasets. Weighted gene co-expression network analysis shows that one gene module was associated with a better prognosis of patients with the GCB subtype. Through the construction of a regulatory network and qPCR verification of clinical samples and cell lines, miR-129-5p was identified as an important differential miRNA between the ABC and GCB subtypes. The negative relationship between miR-129-5p and ARID3A in DLBCL was confirmed using luciferase reporter assays. Overexpression of miR-129-5p and knockdown of ARID3A inhibited the proliferation of SU-DHL-2 (ABC-type) cells and promoted their apoptosis through the JAK and STAT6 signaling pathways. In addition, inhibition of miR-129-5p and overexpression of ARID3A promoted the proliferation and reduced apoptosis of DB and SU-DHL-6 (GCB-type) cells. Inhibition of miR-129-5p and overexpression of ARID3A in DB and SU-DHL-6 promoted immune escape by increasing PD-L1 expression, which was transcriptionally activated by ARID3A. In conclusion, we showed for the first time that the mir-129-5P/ARID3A negative feedback loop modulates DLBCL progression and immune evasion by regulating PD-1/PD-L1.
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Affiliation(s)
- Weili Zheng
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical Center of Hematology, Fujian Institute of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fujian Medical University Union Hospital, Fuzhou, China
| | - Guilan Lai
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical Center of Hematology, Fujian Institute of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fujian Medical University Union Hospital, Fuzhou, China
| | - Qiaochu Lin
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical Center of Hematology, Fujian Institute of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fujian Medical University Union Hospital, Fuzhou, China
| | - Mohammed Awal Issah
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical Center of Hematology, Fujian Institute of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fujian Medical University Union Hospital, Fuzhou, China
| | - Haiying Fu
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical Center of Hematology, Fujian Institute of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fujian Medical University Union Hospital, Fuzhou, China
| | - Jianzhen Shen
- Fujian Provincial Key Laboratory on Hematology, Fujian Medical Center of Hematology, Fujian Institute of Hematology, Clinical Research Center for Hematological Malignancies of Fujian Province, Fujian Medical University Union Hospital, Fuzhou, China
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11
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Wang L, Sun X, Jin C, Fan Y, Xue F. Identification of Tumor Microenvironment-Related Prognostic Biomarkers for Ovarian Serous Cancer 3-Year Mortality Using Targeted Maximum Likelihood Estimation: A TCGA Data Mining Study. Front Genet 2021; 12:625145. [PMID: 34149794 PMCID: PMC8211425 DOI: 10.3389/fgene.2021.625145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 05/11/2021] [Indexed: 02/01/2023] Open
Abstract
Ovarian serous cancer (OSC) is one of the leading causes of death across the world. The role of the tumor microenvironment (TME) in OSC has received increasing attention. Targeted maximum likelihood estimation (TMLE) is developed under a counterfactual framework to produce effect estimation for both the population level and individual level. In this study, we aim to identify TME-related genes and using the TMLE method to estimate their effects on the 3-year mortality of OSC. In total, 285 OSC patients from the TCGA database constituted the studying population. ESTIMATE algorithm was implemented to evaluate immune and stromal components in TME. Differential analysis between high-score and low-score groups regarding ImmuneScore and StromalScore was performed to select shared differential expressed genes (DEGs). Univariate logistic regression analysis was followed to evaluate associations between DEGs and clinical pathologic factors with 3-year mortality. TMLE analysis was conducted to estimate the average effect (AE), individual effect (IE), and marginal odds ratio (MOR). The validation was performed using three datasets from Gene Expression Omnibus (GEO) database. Additionally, 355 DEGs were selected after differential analysis, and 12 genes from DEGs were significant after univariate logistic regression. Four genes remained significant after TMLE analysis. In specific, ARID3C and FREM2 were negatively correlated with OSC 3-year mortality. CROCC2 and PTF1A were positively correlated with OSC 3-year mortality. Combining of ESTIMATE algorithm and TMLE algorithm, we identified four TME-related genes in OSC. AEs were estimated to provide averaged effects based on the population level, while IEs were estimated to provide individualized effects and may be helpful for precision medicine.
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Affiliation(s)
- Lu Wang
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Xiaoru Sun
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Chuandi Jin
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Yue Fan
- Key Laboratory of Trace Elements and Endemic Diseases, National Health and Family Planning Commission, School of Public Health, Xi’an Jiaotong University, Xi’an, China
| | - Fuzhong Xue
- Institute for Medical Dataology, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Biostatistics, School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan, China
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12
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Jackson TR, Ling RE, Roy A. The Origin of B-cells: Human Fetal B Cell Development and Implications for the Pathogenesis of Childhood Acute Lymphoblastic Leukemia. Front Immunol 2021; 12:637975. [PMID: 33679795 PMCID: PMC7928347 DOI: 10.3389/fimmu.2021.637975] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/28/2021] [Indexed: 12/27/2022] Open
Abstract
Human B-lymphopoiesis is a dynamic life-long process that starts in utero by around six post-conception weeks. A detailed understanding of human fetal B-lymphopoiesis and how it changes in postnatal life is vital for building a complete picture of normal B-lymphoid development through ontogeny, and its relevance in disease. B-cell acute lymphoblastic leukemia (B-ALL) is one of the most common cancers in children, with many of the leukemia-initiating events originating in utero. It is likely that the biology of B-ALL, including leukemia initiation, maintenance and progression depends on the developmental stage and type of B-lymphoid cell in which it originates. This is particularly important for early life leukemias, where specific characteristics of fetal B-cells might be key to determining how the disease behaves, including response to treatment. These cellular, molecular and/or epigenetic features are likely to change with age in a cell intrinsic and/or microenvironment directed manner. Most of our understanding of fetal B-lymphopoiesis has been based on murine data, but many recent studies have focussed on characterizing human fetal B-cell development, including functional and molecular assays at a single cell level. In this mini-review we will give a short overview of the recent advances in the understanding of human fetal B-lymphopoiesis, including its relevance to infant/childhood leukemia, and highlight future questions in the field.
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Affiliation(s)
- Thomas R Jackson
- Department of Paediatrics and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Rebecca E Ling
- Department of Paediatrics and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Anindita Roy
- Department of Paediatrics and MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom.,National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, Oxford, United Kingdom
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13
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Morales-Martinez M, Lichtenstein A, Vega MI. Function of Deptor and its roles in hematological malignancies. Aging (Albany NY) 2021; 13:1528-1564. [PMID: 33412518 PMCID: PMC7834987 DOI: 10.18632/aging.202462] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 12/10/2020] [Indexed: 12/12/2022]
Abstract
Deptor is a protein that interacts with mTOR and that belongs to the mTORC1 and mTORC2 complexes. Deptor is capable of inhibiting the kinase activity of mTOR. It is well known that the mTOR pathway is involved in various signaling pathways that are involved with various biological processes such as cell growth, apoptosis, autophagy, and the ER stress response. Therefore, Deptor, being a natural inhibitor of mTOR, has become very important in its study. Because of this, it is important to research its role regarding the development and progression of human malignancies, especially in hematologic malignancies. Due to its variation in expression in cancer, it has been suggested that Deptor can act as an oncogene or tumor suppressor depending on the cellular or tissue context. This review discusses recent advances in its transcriptional and post-transcriptional regulation of Deptor. As well as the advances regarding the activities of Deptor in hematological malignancies, its possible role as a biomarker, and its possible clinical relevance in these malignancies.
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Affiliation(s)
- Mario Morales-Martinez
- Molecular Signal Pathway in Cancer Laboratory, UIMEO, Oncology Hospital, Siglo XXI National Medical Center, IMSS, México City, México
| | - Alan Lichtenstein
- Department of Medicine, Hematology-Oncology Division, Greater Los Angeles VA Healthcare Center, UCLA Medical Center, Jonsson Comprehensive Cancer Center, Los Angeles, CA 90024, USA
| | - Mario I Vega
- Molecular Signal Pathway in Cancer Laboratory, UIMEO, Oncology Hospital, Siglo XXI National Medical Center, IMSS, México City, México.,Department of Medicine, Hematology-Oncology Division, Greater Los Angeles VA Healthcare Center, UCLA Medical Center, Jonsson Comprehensive Cancer Center, Los Angeles, CA 90024, USA
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14
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Tang J, Yang L, Li Y, Ning X, Chaulagain A, Wang T, Wang D. ARID3A promotes the development of colorectal cancer by upregulating AURKA. Carcinogenesis 2020; 42:578-586. [PMID: 33165575 DOI: 10.1093/carcin/bgaa118] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 10/27/2020] [Accepted: 10/31/2020] [Indexed: 02/07/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common malignant tumours, and its morbidity and mortality rates are relatively high. However, the aetiology and pathogenesis of CRC have not been clearly elucidated to date. AT-rich interaction domain 3A (ARID3A) is a member of the ARID3 family and a transcription factor that can bind to specific DNA sites to regulate gene expression. It was reported that ARID3A is involved in various biological processes and may be related to carcinogenesis. In this study, by assessing the mRNA level of ARID3A in TCGA database, we found that ARID3A expression increased in CRC tissues, and proposed that ARID3A could act as a tumour-promoting factor in the development of CRC. To verify this hypothesis, we used cell proliferation, migration and invasion assays to assess the effect of ARID3A on CRC cells. We revealed that ARID3A overexpression enhanced tumour cell proliferation, migration and invasion. ARID3A could target Aurora kinase A (AURKA) to facilitate the malignant phenotype of CRC cells, and patients with a higher ratio of AURKA and ARID3A had a better overall survival. Conclusively, this study showed that ARID3A targeted AURKA to facilitate the development of CRC. The ratio of ARID3A and AURKA could be used as a potential biomarker to predict prognosis, providing a new strategy for the diagnosis and prognosis of CRC.
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Affiliation(s)
- Jing Tang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Department of Pathology, Harbin Medical University, Harbin, China
| | - Lirui Yang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Yafei Li
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Xuelian Ning
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Anita Chaulagain
- Department of Microbiology, Harbin Medical University, Harbin, China
| | - Tianzhen Wang
- Department of Pathology, Harbin Medical University, Harbin, China
| | - Dong Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.,Dermatology Hospital, Southern Medical University, Guangzhou, China.,Center for Informational Biology, University of Electronic Science and Technology of China, Chengdu, China
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15
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Gojo J, Englinger B, Jiang L, Hübner JM, Shaw ML, Hack OA, Madlener S, Kirchhofer D, Liu I, Pyrdol J, Hovestadt V, Mazzola E, Mathewson ND, Trissal M, Lötsch D, Dorfer C, Haberler C, Halfmann A, Mayr L, Peyrl A, Geyeregger R, Schwalm B, Mauermann M, Pajtler KW, Milde T, Shore ME, Geduldig JE, Pelton K, Czech T, Ashenberg O, Wucherpfennig KW, Rozenblatt-Rosen O, Alexandrescu S, Ligon KL, Pfister SM, Regev A, Slavc I, Berger W, Suvà ML, Kool M, Filbin MG. Single-Cell RNA-Seq Reveals Cellular Hierarchies and Impaired Developmental Trajectories in Pediatric Ependymoma. Cancer Cell 2020; 38:44-59.e9. [PMID: 32663469 PMCID: PMC7479515 DOI: 10.1016/j.ccell.2020.06.004] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 03/26/2020] [Accepted: 06/03/2020] [Indexed: 02/07/2023]
Abstract
Ependymoma is a heterogeneous entity of central nervous system tumors with well-established molecular groups. Here, we apply single-cell RNA sequencing to analyze ependymomas across molecular groups and anatomic locations to investigate their intratumoral heterogeneity and developmental origins. Ependymomas are composed of a cellular hierarchy initiating from undifferentiated populations, which undergo impaired differentiation toward three lineages of neuronal-glial fate specification. While prognostically favorable groups of ependymoma predominantly harbor differentiated cells, aggressive groups are enriched for undifferentiated cell populations. The delineated transcriptomic signatures correlate with patient survival and define molecular dependencies for targeted treatment approaches. Taken together, our analyses reveal a developmental hierarchy underlying ependymomas relevant to biological and clinical behavior.
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Affiliation(s)
- Johannes Gojo
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Bernhard Englinger
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Li Jiang
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jens M Hübner
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - McKenzie L Shaw
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Olivia A Hack
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Sibylle Madlener
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Dominik Kirchhofer
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Ilon Liu
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Jason Pyrdol
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Volker Hovestadt
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Emanuele Mazzola
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Nathan D Mathewson
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Maria Trissal
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Daniela Lötsch
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria; Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria; Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Christian Dorfer
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Christine Haberler
- Division of Neuropathology and Neurochemistry, Department of Neurology, Medical University of Vienna, 1090 Vienna, Austria
| | - Angela Halfmann
- Clinical Cell Biology, Children's Cancer Research Institute (CCRI), 1090 Vienna, Austria
| | - Lisa Mayr
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Andreas Peyrl
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Rene Geyeregger
- Clinical Cell Biology, Children's Cancer Research Institute (CCRI), 1090 Vienna, Austria
| | - Benjamin Schwalm
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Monica Mauermann
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Kristian W Pajtler
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Till Milde
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Marni E Shore
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jack E Geduldig
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Kristine Pelton
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Thomas Czech
- Department of Neurosurgery, Medical University of Vienna, 1090 Vienna, Austria
| | - Orr Ashenberg
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Kai W Wucherpfennig
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute and Harvard Medical School, Boston, MA 02215, USA
| | - Orit Rozenblatt-Rosen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Sanda Alexandrescu
- Department of Pathology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Keith L Ligon
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA 02215, USA; Department of Pathology, Brigham and Women's Hospital, Boston Children's Hospital, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Stefan M Pfister
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Department of Paediatric Haematology and Oncology, Heidelberg University Hospital, 69120 Heidelberg, Germany
| | - Aviv Regev
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
| | - Walter Berger
- Institute of Cancer Research, Comprehensive Cancer Center, Medical University of Vienna, 1090 Vienna, Austria
| | - Mario L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Marcel Kool
- Hopp Children's Cancer Center (KiTZ), 69120 Heidelberg, Germany; Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany; Princess Máxima Center for Pediatric Oncology, 3584 CS Utrecht, the Netherlands
| | - Mariella G Filbin
- Department of Pediatric Oncology, Dana-Farber Boston Children's Cancer and Blood Disorders Center, Boston, MA 02215, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
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