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Ma S, Pan X, Gan J, Guo X, He J, Hu H, Wang Y, Ning S, Zhi H. DNA methylation heterogeneity attributable to a complex tumor immune microenvironment prompts prognostic risk in glioma. Epigenetics 2024; 19:2318506. [PMID: 38439715 PMCID: PMC10936651 DOI: 10.1080/15592294.2024.2318506] [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: 07/26/2023] [Accepted: 02/07/2024] [Indexed: 03/06/2024] Open
Abstract
Gliomas are malignant tumours of the human nervous system with different World Health Organization (WHO) classifications, glioblastoma (GBM) with higher grade and are more malignant than lower-grade glioma (LGG). To dissect how the DNA methylation heterogeneity in gliomas is influenced by the complex cellular composition of the tumour immune microenvironment, we first compared the DNA methylation profiles of purified human immune cells and bulk glioma tissue, stratifying three tumour immune microenvironmental subtypes for GBM and LGG samples from The Cancer Genome Atlas (TCGA). We found that more intermediate methylation sites were enriched in glioma tumour tissues, and used the Proportion of sites with Intermediate Methylation (PIM) to compare intertumoral DNA methylation heterogeneity. A larger PIM score reflected stronger DNA methylation heterogeneity. Enhanced DNA methylation heterogeneity was associated with stronger immune cell infiltration, better survival rates, and slower tumour progression in glioma patients. We then created a Cell-type-associated DNA Methylation Heterogeneity Contribution (CMHC) score to explore the impact of different immune cell types on heterogeneous CpG site (CpGct) in glioma tissues. We identified eight prognosis-related CpGct to construct a risk score: the Cell-type-associated DNA Methylation Heterogeneity Risk (CMHR) score. CMHR was positively correlated with cytotoxic T-lymphocyte infiltration (CTL), and showed better predictive performance for IDH status (AUC = 0.96) and glioma histological phenotype (AUC = 0.81). Furthermore, DNA methylation alterations of eight CpGct might be related to drug treatments of gliomas. In conclusion, we indicated that DNA methylation heterogeneity is associated with a complex tumour immune microenvironment, glioma phenotype, and patient's prognosis.
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Affiliation(s)
- Shuangyue Ma
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
- Liangzhu Laboratory, Zhejiang University, Hangzhou, China
| | - Xu Pan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jing Gan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Xiaxin Guo
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Jiaheng He
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haoyu Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yuncong Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Shangwei Ning
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Hui Zhi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
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Hendriksen JD, Locallo A, Maarup S, Debnath O, Ishaque N, Hasselbach B, Skjøth-Rasmussen J, Yde CW, Poulsen HS, Lassen U, Weischenfeldt J. Immunotherapy drives mesenchymal tumor cell state shift and TME immune response in glioblastoma patients. Neuro Oncol 2024; 26:1453-1466. [PMID: 38695342 PMCID: PMC11300009 DOI: 10.1093/neuonc/noae085] [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] [Indexed: 08/07/2024] Open
Abstract
BACKGROUND Glioblastoma is a highly aggressive type of brain tumor for which there is no curative treatment available. Immunotherapies have shown limited responses in unselected patients, and there is an urgent need to identify mechanisms of treatment resistance to design novel therapy strategies. METHODS Here we investigated the phenotypic and transcriptional dynamics at single-cell resolution during nivolumab immune checkpoint treatment of glioblastoma patients. RESULTS We present the integrative paired single-cell RNA-seq analysis of 76 tumor samples from patients in a clinical trial of the PD-1 inhibitor nivolumab and untreated patients. We identify a distinct aggressive phenotypic signature in both tumor cells and the tumor microenvironment in response to nivolumab. Moreover, nivolumab-treatment was associated with an increased transition to mesenchymal stem-like tumor cells, and an increase in TAMs and exhausted and proliferative T cells. We verify and extend our findings in large external glioblastoma dataset (n = 298), develop a latent immune signature and find 18% of primary glioblastoma samples to be latent immune, associated with mesenchymal tumor cell state and TME immune response. Finally, we show that latent immune glioblastoma patients are associated with shorter overall survival following immune checkpoint treatment (P = .0041). CONCLUSIONS We find a resistance mechanism signature in one fifth of glioblastoma patients associated with a tumor-cell transition to a more aggressive mesenchymal-like state, increase in TAMs and proliferative and exhausted T cells in response to immunotherapy. These patients may instead benefit from neuro-oncology therapies targeting mesenchymal tumor cells.
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Affiliation(s)
- Josephine D Hendriksen
- The Finsen Laboratory, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- The DCCC Brain Tumor Center, Danish Comprehensive Cancer Center, Denmark
| | - Alessio Locallo
- The Finsen Laboratory, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- The DCCC Brain Tumor Center, Danish Comprehensive Cancer Center, Denmark
| | - Simone Maarup
- The DCCC Brain Tumor Center, Danish Comprehensive Cancer Center, Denmark
- Department of Radiation Biology, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark
| | - Olivia Debnath
- Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Naveed Ishaque
- Berlin Institute of Health at Charité—Universitätsmedizin Berlin, Digital Health Center, Berlin, Germany
| | - Benedikte Hasselbach
- The DCCC Brain Tumor Center, Danish Comprehensive Cancer Center, Denmark
- Department of Oncology, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark
| | - Jane Skjøth-Rasmussen
- The DCCC Brain Tumor Center, Danish Comprehensive Cancer Center, Denmark
- Department of Neurosurgery, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark
| | - Christina Westmose Yde
- Department of Genomic Medicine, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark
| | - Hans S Poulsen
- The DCCC Brain Tumor Center, Danish Comprehensive Cancer Center, Denmark
- Department of Radiation Biology, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark
| | - Ulrik Lassen
- The DCCC Brain Tumor Center, Danish Comprehensive Cancer Center, Denmark
- Department of Oncology, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark
- Department of Clinical Medicine, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark
| | - Joachim Weischenfeldt
- The Finsen Laboratory, Copenhagen University Hospital—Rigshospitalet, Copenhagen, Denmark
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark
- The DCCC Brain Tumor Center, Danish Comprehensive Cancer Center, Denmark
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3
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Fazzari E, Azizad DJ, Yu K, Ge W, Li MX, Nano PR, Kan RL, Tum HA, Tse C, Bayley NA, Haka V, Cadet D, Perryman T, Soto JA, Wick B, Raleigh DR, Crouch EE, Patel KS, Liau LM, Deneen B, Nathanson DA, Bhaduri A. Glioblastoma Neurovascular Progenitor Orchestrates Tumor Cell Type Diversity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.24.604840. [PMID: 39091877 PMCID: PMC11291138 DOI: 10.1101/2024.07.24.604840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Glioblastoma (GBM) is the deadliest form of primary brain tumor with limited treatment options. Recent studies have profiled GBM tumor heterogeneity, revealing numerous axes of variation that explain the molecular and spatial features of the tumor. Here, we seek to bridge descriptive characterization of GBM cell type heterogeneity with the functional role of individual populations within the tumor. Our lens leverages a gene program-centric meta-atlas of published transcriptomic studies to identify commonalities between diverse tumors and cell types in order to decipher the mechanisms that drive them. This approach led to the discovery of a tumor-derived stem cell population with mixed vascular and neural stem cell features, termed a neurovascular progenitor (NVP). Following in situ validation and molecular characterization of NVP cells in GBM patient samples, we characterized their function in vivo. Genetic depletion of NVP cells resulted in altered tumor cell composition, fewer cycling cells, and extended survival, underscoring their critical functional role. Clonal analysis of primary patient tumors in a human organoid tumor transplantation system demonstrated that the NVP has dual potency, generating both neuronal and vascular tumor cells. Although NVP cells comprise a small fraction of the tumor, these clonal analyses demonstrated that they strongly contribute to the total number of cycling cells in the tumor and generate a defined subset of the whole tumor. This study represents a paradigm by which cell type-specific interrogation of tumor populations can be used to study functional heterogeneity and therapeutically targetable vulnerabilities of GBM.
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Affiliation(s)
- Elisa Fazzari
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Daria J Azizad
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Kwanha Yu
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Weihong Ge
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Matthew X Li
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Patricia R Nano
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Ryan L Kan
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Hong A Tum
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Christopher Tse
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nicholas A Bayley
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Vjola Haka
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Dimitri Cadet
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Travis Perryman
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Jose A Soto
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Brittney Wick
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California, USA
- Department of Pathology, University of California San Francisco, San Francisco, California, USA
| | - Elizabeth E Crouch
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, USA
- The Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA, USA
| | - Kunal S Patel
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Linda M Liau
- Department of Neurosurgery, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
| | - Benjamin Deneen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - David A Nathanson
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Aparna Bhaduri
- Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, California, Los Angeles, CA, USA
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4
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Richardson TE, Walker JM, Hambardzumyan D, Brem S, Hatanpaa KJ, Viapiano MS, Pai B, Umphlett M, Becher OJ, Snuderl M, McBrayer SK, Abdullah KG, Tsankova NM. Genetic and epigenetic instability as an underlying driver of progression and aggressive behavior in IDH-mutant astrocytoma. Acta Neuropathol 2024; 148:5. [PMID: 39012509 PMCID: PMC11252228 DOI: 10.1007/s00401-024-02761-7] [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: 05/23/2024] [Revised: 06/28/2024] [Accepted: 06/29/2024] [Indexed: 07/17/2024]
Abstract
In recent years, the classification of adult-type diffuse gliomas has undergone a revolution, wherein specific molecular features now represent defining diagnostic criteria of IDH-wild-type glioblastomas, IDH-mutant astrocytomas, and IDH-mutant 1p/19q-codeleted oligodendrogliomas. With the introduction of the 2021 WHO CNS classification, additional molecular alterations are now integrated into the grading of these tumors, given equal weight to traditional histologic features. However, there remains a great deal of heterogeneity in patient outcome even within these established tumor subclassifications that is unexplained by currently codified molecular alterations, particularly in the IDH-mutant astrocytoma category. There is also significant intercellular genetic and epigenetic heterogeneity and plasticity with resulting phenotypic heterogeneity, making these tumors remarkably adaptable and robust, and presenting a significant barrier to the design of effective therapeutics. Herein, we review the mechanisms and consequences of genetic and epigenetic instability, including chromosomal instability (CIN), microsatellite instability (MSI)/mismatch repair (MMR) deficits, and epigenetic instability, in the underlying biology, tumorigenesis, and progression of IDH-mutant astrocytomas. We also discuss the contribution of recent high-resolution transcriptomics studies toward defining tumor heterogeneity with single-cell resolution. While intratumoral heterogeneity is a well-known feature of diffuse gliomas, the contribution of these various processes has only recently been considered as a potential driver of tumor aggressiveness. CIN has an independent, adverse effect on patient survival, similar to the effect of histologic grade and homozygous CDKN2A deletion, while MMR mutation is only associated with poor overall survival in univariate analysis but is highly correlated with higher histologic/molecular grade and other aggressive features. These forms of genomic instability, which may significantly affect the natural progression of these tumors, response to therapy, and ultimately clinical outcome for patients, are potentially measurable features which could aid in diagnosis, grading, prognosis, and development of personalized therapeutics.
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Affiliation(s)
- Timothy E Richardson
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA.
| | - Jamie M Walker
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Dolores Hambardzumyan
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
- Department of Neurosurgery, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
| | - Steven Brem
- Department of Neurosurgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
- Glioblastoma Translational Center of Excellence, Abramson Cancer Center, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Kimmo J Hatanpaa
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Mariano S Viapiano
- Department of Neuroscience and Physiology, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
- Department of Neurosurgery, State University of New York, Upstate Medical University, Syracuse, NY, 13210, USA
| | - Balagopal Pai
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Melissa Umphlett
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
| | - Oren J Becher
- Department of Oncological Sciences, The Tisch Cancer Institute, Mount Sinai Icahn School of Medicine, New York, NY, 10029, USA
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Matija Snuderl
- Department of Pathology, New York University Langone Health, New York, NY, 10016, USA
| | - Samuel K McBrayer
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
- Children's Medical Center Research Institute, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Kalil G Abdullah
- Department of Neurosurgery, University of Pittsburgh School of Medicine, 200 Lothrop St, Pittsburgh, PA, 15213, USA
- Hillman Comprehensive Cancer Center, University of Pittsburgh Medical Center, 5115 Centre Ave, Pittsburgh, PA, 15232, USA
| | - Nadejda M Tsankova
- Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, 1468 Madison Avenue, Annenberg Building, 15.238, New York, NY, 10029, USA
- Nash Family Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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5
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Yang Y, Jin X, Xie Y, Ning C, Ai Y, Wei H, Xu X, Ge X, Yi T, Huang Q, Yang X, Jiang T, Wang X, Piao Y, Jin X. The CEBPB + glioblastoma subcluster specifically drives the formation of M2 tumor-associated macrophages to promote malignancy growth. Theranostics 2024; 14:4107-4126. [PMID: 38994023 PMCID: PMC11234274 DOI: 10.7150/thno.93473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Accepted: 06/24/2024] [Indexed: 07/13/2024] Open
Abstract
Rationale: The heterogeneity of tumor cells within the glioblastoma (GBM) microenvironment presents a complex challenge in curbing GBM progression. Understanding the specific mechanisms of interaction between different GBM cell subclusters and non-tumor cells is crucial. Methods: In this study, we utilized a comprehensive approach integrating glioma single-cell and spatial transcriptomics. This allowed us to examine the molecular interactions and spatial localization within GBM, focusing on a specific tumor cell subcluster, GBM subcluster 6, and M2-type tumor-associated macrophages (M2 TAMs). Results: Our analysis revealed a significant correlation between a specific tumor cell subcluster, GBM cluster 6, and M2-type TAMs. Further in vitro and in vivo experiments demonstrated the specific regulatory role of the CEBPB transcriptional network in GBM subcluster 6, which governs its tumorigenicity, recruitment of M2 TAMs, and polarization. This regulation involves molecules such as MCP1 for macrophage recruitment and the SPP1-Integrin αvβ1-Akt signaling pathway for M2 polarization. Conclusion: Our findings not only deepen our understanding of the formation of M2 TAMs, particularly highlighting the differential roles played by heterogeneous cells within GBM in this process, but also provided new insights for effectively controlling the malignant progression of GBM.
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Affiliation(s)
- Yongchang Yang
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
- Tianjin Medical University, Tianjin 300060, China
| | - Xingyu Jin
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
- Tianjin Medical University, Tianjin 300060, China
| | - Yang Xie
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
- Tianjin Medical University, Tianjin 300060, China
| | - Chunlan Ning
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
- Tianjin Medical University, Tianjin 300060, China
| | - Yiding Ai
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
- Tianjin Medical University, Tianjin 300060, China
| | - Haotian Wei
- Tianjin Medical University, Tianjin 300060, China
| | - Xing Xu
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Xianglian Ge
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Tailong Yi
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Qiang Huang
- Department of Neurosurgery, Tianjin Medical University General Hospital, Tianjin, 300052, China
| | - Xuejun Yang
- Department of Neurosurgery, Beijing Tsinghua Changgung Hospital, Tsinghua University, Beijing, People's Republic of China
| | - Tao Jiang
- Beijing Neurosurgical Institute, Capital Medical University, Beijing, China
| | - Xiaoguang Wang
- Department of Neuro-Oncology and Neurosurgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin China
| | - Yingzhe Piao
- Department of Neuro-Oncology and Neurosurgery, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin China
| | - Xun Jin
- Department of Biochemistry and Molecular Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
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6
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Li C, Long L, Wang Y, Chi X, Zhang P, Zhang Y, Ji N. Constitutive type-1 interferons signaling activity in malignant gliomas. J Neurooncol 2024; 168:381-391. [PMID: 38789844 DOI: 10.1007/s11060-024-04601-w] [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: 12/31/2023] [Accepted: 02/07/2024] [Indexed: 05/26/2024]
Abstract
PURPOSE Recent studies revealed a pro-tumor effect of constitutive Type-1 interferons (IFN-I) production and the downstream signaling activity in several malignancies. In contrast, heterogeneity and clinical significance of the signaling activity in gliomas remain unknown. Thus, we aimed to depict the heterogeneity and clinical significance of constitutive Type-1 interferon (IFN-I) production and the downstream signaling activity in gliomas. METHODS We utilized multiplex immunofluorescence (mIF) on a 364 gliomas tissue microarray from our cohort. Moreover, we conducted bioinformatic analyses on the Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA) databases to investigate the heterogeneity and clinical significance of constitutive IFN-I signaling activity in gliomas. RESULTS We observed high heterogeneity of the constitutive IFN-I signaling activity among glioma subtypes. Signaling increased with the WHO malignancy grade while decreasing in the gliomas with IDH mutations. Additionally, high IFN-I activity served as an independent predictor of unfavorable outcomes, and global DNA hypermethylation in IDH-mutant gliomas was associated with decreased IFN-I signaling activity. Positive correlations were observed between the IFN-I activity and glioma-associated inflammation, encompassing both anti-tumor and pro-tumor immune responses. Furthermore, the IFN-I activity varied significantly among tumor and immune cells in the glioma microenvironment (GME). Notably, a distinct pattern of IFN-I signaling activity distribution in GME cells was observed among glioma subtypes, and the pattern was independently associated with patient overall survival. CONCLUSIONS Constitutive IFN-I signaling activity varies significantly among glioma subtypes and represents a potential indicator for increased glioma inflammation and unfavorable clinical outcomes.
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Affiliation(s)
- Chunzhao Li
- Department of Neurosurgery, Fengtai District, Beijing Tiantan Hospital, Capital Medical University, Nan Si Huan Xi Lu 119, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Lang Long
- Department of Neurosurgery, Fengtai District, Beijing Tiantan Hospital, Capital Medical University, Nan Si Huan Xi Lu 119, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Yi Wang
- Department of Neurosurgery, Fengtai District, Beijing Tiantan Hospital, Capital Medical University, Nan Si Huan Xi Lu 119, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, China
| | - Xiaohan Chi
- Department of Neurosurgery, Fengtai District, Beijing Tiantan Hospital, Capital Medical University, Nan Si Huan Xi Lu 119, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Peng Zhang
- Department of Neurosurgery, Fengtai District, Beijing Tiantan Hospital, Capital Medical University, Nan Si Huan Xi Lu 119, Beijing, 100070, China
- China National Clinical Research Center for Neurological Diseases, Beijing, China
| | - Yang Zhang
- Department of Neurosurgery, Fengtai District, Beijing Tiantan Hospital, Capital Medical University, Nan Si Huan Xi Lu 119, Beijing, 100070, China.
- China National Clinical Research Center for Neurological Diseases, Beijing, China.
| | - Nan Ji
- Department of Neurosurgery, Fengtai District, Beijing Tiantan Hospital, Capital Medical University, Nan Si Huan Xi Lu 119, Beijing, 100070, China.
- China National Clinical Research Center for Neurological Diseases, Beijing, China.
- Beijing Advanced Innovation Center for Big Data-Based Precision Medicine, Beihang University, Beijing, China.
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7
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Niu X, Liu W, Zhang Y, Liu J, Zhang J, Li B, Qiu Y, Zhao P, Wang Z, Wang Z. Cancer plasticity in therapy resistance: Mechanisms and novel strategies. Drug Resist Updat 2024; 76:101114. [PMID: 38924995 DOI: 10.1016/j.drup.2024.101114] [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: 04/17/2024] [Revised: 06/12/2024] [Accepted: 06/15/2024] [Indexed: 06/28/2024]
Abstract
Therapy resistance poses a significant obstacle to effective cancer treatment. Recent insights into cell plasticity as a new paradigm for understanding resistance to treatment: as cancer progresses, cancer cells experience phenotypic and molecular alterations, corporately known as cell plasticity. These alterations are caused by microenvironment factors, stochastic genetic and epigenetic changes, and/or selective pressure engendered by treatment, resulting in tumor heterogeneity and therapy resistance. Increasing evidence suggests that cancer cells display remarkable intrinsic plasticity and reversibly adapt to dynamic microenvironment conditions. Dynamic interactions between cell states and with the surrounding microenvironment form a flexible tumor ecosystem, which is able to quickly adapt to external pressure, especially treatment. Here, this review delineates the formation of cancer cell plasticity (CCP) as well as its manipulation of cancer escape from treatment. Furthermore, the intrinsic and extrinsic mechanisms driving CCP that promote the development of therapy resistance is summarized. Novel treatment strategies, e.g., inhibiting or reversing CCP is also proposed. Moreover, the review discusses the multiple lines of ongoing clinical trials globally aimed at ameliorating therapy resistance. Such advances provide directions for the development of new treatment modalities and combination therapies against CCP in the context of therapy resistance.
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Affiliation(s)
- Xing Niu
- China Medical University, Shenyang, Liaoning 110122, China; Experimental Center of BIOQGene, YuanDong International Academy Of Life Sciences, 999077, Hong Kong, China
| | - Wenjing Liu
- Medical Oncology Department of Thoracic Cancer (2), Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
| | - Yinling Zhang
- Department of Oncology Radiotherapy 1, Qingdao Central Hospital, University of Health and Rehabilitation Sciences, Qingdao, Shandong 266042, China
| | - Jing Liu
- Department of Oncology, Shengjing Hospital of China Medical University, Shenyang, Liaoning 110004, China
| | - Jianjun Zhang
- Department of Gastric Surgery, Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
| | - Bo Li
- Department of Orthopedics, Beijing Luhe Hospital, Capital Medical University, Beijing 101149, China
| | - Yue Qiu
- Department of Digestive Diseases 1, Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
| | - Peng Zhao
- Department of Medical Imaging, Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China
| | - Zhongmiao Wang
- Department of Digestive Diseases 1, Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China.
| | - Zhe Wang
- Department of Digestive Diseases 1, Cancer Hospital of China Medical University, Cancer Hospital of Dalian University of Technology, Liaoning Cancer Hospital & Institute, Shenyang, Liaoning 110042, China.
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8
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Huang K, Xu Y, Feng T, Lan H, Ling F, Xiang H, Liu Q. The Advancement and Application of the Single-Cell Transcriptome in Biological and Medical Research. BIOLOGY 2024; 13:451. [PMID: 38927331 PMCID: PMC11200756 DOI: 10.3390/biology13060451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/11/2024] [Accepted: 06/17/2024] [Indexed: 06/28/2024]
Abstract
Single-cell RNA sequencing technology (scRNA-seq) has been steadily developing since its inception in 2009. Unlike bulk RNA-seq, scRNA-seq identifies the heterogeneity of tissue cells and reveals gene expression changes in individual cells at the microscopic level. Here, we review the development of scRNA-seq, which has gone through iterations of reverse transcription, in vitro transcription, smart-seq, drop-seq, 10 × Genomics, and spatial single-cell transcriptome technologies. The technology of 10 × Genomics has been widely applied in medicine and biology, producing rich research results. Furthermore, this review presents a summary of the analytical process for single-cell transcriptome data and its integration with other omics analyses, including genomes, epigenomes, proteomes, and metabolomics. The single-cell transcriptome has a wide range of applications in biology and medicine. This review analyzes the applications of scRNA-seq in cancer, stem cell research, developmental biology, microbiology, and other fields. In essence, scRNA-seq provides a means of elucidating gene expression patterns in single cells, thereby offering a valuable tool for scientific research. Nevertheless, the current single-cell transcriptome technology is still imperfect, and this review identifies its shortcomings and anticipates future developments. The objective of this review is to facilitate a deeper comprehension of scRNA-seq technology and its applications in biological and medical research, as well as to identify avenues for its future development in alignment with practical needs.
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Affiliation(s)
- Kongwei Huang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510641, China
| | - Yixue Xu
- Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530005, China;
| | - Tong Feng
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular Imaging, Center for Artificial Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Hong Lan
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Fei Ling
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510641, China
| | - Hai Xiang
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan 528225, China
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9
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Johnson KC, Tien AC, Jiang J, McNamara J, Chang YW, Montgomery C, DeSantis A, Elena-Sanchez L, Fujita Y, Kim S, Spitzer A, Gabriel P, Flynn WF, Courtois ET, Hong A, Harmon J, Umemura Y, Tovmasyan A, Li J, Mehta S, Verhaak R, Sanai N. Single nucleus transcriptomics, pharmacokinetics, and pharmacodynamics of combined CDK4/6 and mTOR inhibition in a phase 0/1 trial of recurrent high-grade glioma. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.07.24308439. [PMID: 38883740 PMCID: PMC11178017 DOI: 10.1101/2024.06.07.24308439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2024]
Abstract
Outcomes for adult patients with a high-grade glioma continue to be dismal and new treatment paradigms are urgently needed. To optimize the opportunity for discovery, we performed a phase 0/1 dose-escalation clinical trial that investigated tumor pharmacokinetics, pharmacodynamics, and single nucleus transcriptomics following combined ribociclib (CDK4/6 inhibitor) and everolimus (mTOR inhibitor) treatment in recurrent high-grade glioma. Patients with a recurrent high-grade glioma (n = 24) harboring 1) CDKN2A / B deletion or CDK4 / 6 amplification, 2) PTEN loss or PIK3CA mutations, and 3) wild-type retinoblastoma protein (Rb) were enrolled. Patients received neoadjuvant ribociclib and everolimus treatment and no dose-limiting toxicities were observed. The median unbound ribociclib concentrations in Gadolinium non-enhancing tumor regions were 170 nM (range, 65 - 1770 nM) and 634 nM (range, 68 - 2345 nM) in patients receiving 5 days treatment at the daily dose of 400 and 600 mg, respectively. Unbound everolimus concentrations were below the limit of detection (< 0.1 nM) in both enhancing and non-enhancing tumor regions at all dose levels. We identified a significant decrease in MIB1 positive cells suggesting ribociclib-associated cell cycle inhibition. Single nuclei RNAseq (snRNA) based comparisons of 17 IDH-wild-type on-trial recurrences to 31 IDH-wild-type standard of care treated recurrences data demonstrated a significantly lower fraction of cycling and neural progenitor-like (NPC-like) malignant cell populations. We validated the CDK4/6 inhibitor-directed malignant cell state shifts using three patient-derived cell lines. The presented clinical trial highlights the value of integrating pharmacokinetics, pharmacodynamics, and single nucleus transcriptomics to assess treatment effects in phase 0/1 surgical tissues, including malignant cell state shifts. ClinicalTrials.gov identifier: NCT03834740 .
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10
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Whiting FJH, Househam J, Baker AM, Sottoriva A, Graham TA. Phenotypic noise and plasticity in cancer evolution. Trends Cell Biol 2024; 34:451-464. [PMID: 37968225 DOI: 10.1016/j.tcb.2023.10.002] [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: 07/13/2023] [Revised: 09/29/2023] [Accepted: 10/04/2023] [Indexed: 11/17/2023]
Abstract
Non-genetic alterations can produce changes in a cell's phenotype. In cancer, these phenomena can influence a cell's fitness by conferring access to heritable, beneficial phenotypes. Herein, we argue that current discussions of 'phenotypic plasticity' in cancer evolution ignore a salient feature of the original definition: namely, that it occurs in response to an environmental change. We suggest 'phenotypic noise' be used to distinguish non-genetic changes in phenotype that occur independently from the environment. We discuss the conceptual and methodological techniques used to identify these phenomena during cancer evolution. We propose that the distinction will guide efforts to define mechanisms of phenotype change, accelerate translational work to manipulate phenotypes through treatment, and, ultimately, improve patient outcomes.
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Affiliation(s)
| | - Jacob Househam
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Ann-Marie Baker
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
| | - Andrea Sottoriva
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK; Computational Biology Research Centre, Human Technopole, Milan, Italy
| | - Trevor A Graham
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK
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11
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Bumbaca B, Birtwistle MR, Gallo JM. Network Analyses of Brain Tumor Patients' Multiomic Data Reveals Pharmacological Opportunities to Alter Cell State Transitions. RESEARCH SQUARE 2024:rs.3.rs-4391296. [PMID: 38826227 PMCID: PMC11142360 DOI: 10.21203/rs.3.rs-4391296/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Glioblastoma Multiforme (GBM) remains a particularly difficult cancer to treat, and survival outcomes remain poor. In addition to the lack of dedicated drug discovery programs for GBM, extensive intratumor heterogeneity and epigenetic plasticity related to cell-state transitions are major roadblocks to successful drug therapy in GBM. To study these phenomenon, publicly available snRNAseq and bulk RNAseq data from patient samples were used to categorize cells from patients into four cell states (i.e. phenotypes), namely: (i) neural progenitor-like (NPC-like), (ii) oligodendrocyte progenitor-like (OPC-like), (iii) astrocyte- like (AC-like), and (iv) mesenchymal-like (MES-like). Patients were subsequently grouped into subpopulations based on which cell-state was the most dominant in their respective tumor. By incorporating phosphoproteomic measurements from the same patients, a protein-protein interaction network (PPIN) was constructed for each cell state. These four-cell state PPINs were pooled to form a single Boolean network that was used for in silico protein knockout simulations to investigate mechanisms that either promote or prevent cell state transitions. Simulation results were input into a boosted tree machine learning model which predicted the cell states or phenotypes of GBM patients from an independent public data source, the Glioma Longitudinal Analysis (GLASS) Consortium. Combining the simulation results and the machine learning predictions, we generated hypotheses for clinically relevant causal mechanisms of cell state transitions. For example, the transcription factor TFAP2A can be seen to promote a transition from the NPC-like to the MES-like state. Such protein nodes and the associated signaling pathways provide potential drug targets that can be further tested in vitro and support cell state-directed (CSD) therapy.
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Affiliation(s)
- Brandon Bumbaca
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo NY, USA
| | - Marc R Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson SC, USA
- Department of Bioengineering, Clemson University, Clemson SC, USA
| | - James M Gallo
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo NY, USA
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12
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Ho WM, Chen CY, Chiang TW, Chuang TJ. A longer time to relapse is associated with a larger increase in differences between paired primary and recurrent IDH wild-type glioblastomas at both the transcriptomic and genomic levels. Acta Neuropathol Commun 2024; 12:77. [PMID: 38762464 PMCID: PMC11102269 DOI: 10.1186/s40478-024-01790-3] [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: 02/22/2024] [Accepted: 05/05/2024] [Indexed: 05/20/2024] Open
Abstract
Glioblastoma (GBM) is the most common malignant brain tumor in adults, which remains incurable and often recurs rapidly after initial therapy. While large efforts have been dedicated to uncover genomic/transcriptomic alternations associated with the recurrence of GBMs, the evolutionary trajectories of matched pairs of primary and recurrent (P-R) GBMs remain largely elusive. It remains challenging to identify genes associated with time to relapse (TTR) and construct a stable and effective prognostic model for predicting TTR of primary GBM patients. By integrating RNA-sequencing and genomic data from multiple datasets of patient-matched longitudinal GBMs of isocitrate dehydrogenase wild-type (IDH-wt), here we examined the associations of TTR with heterogeneities between paired P-R GBMs in gene expression profiles, tumor mutation burden (TMB), and microenvironment. Our results revealed a positive correlation between TTR and transcriptomic/genomic differences between paired P-R GBMs, higher percentages of non-mesenchymal-to-mesenchymal transition and mesenchymal subtype for patients with a short TTR than for those with a long TTR, a high correlation between paired P-R GBMs in gene expression profiles and TMB, and a negative correlation between the fitting level of such a paired P-R GBM correlation and TTR. According to these observations, we identified 55 TTR-associated genes and thereby constructed a seven-gene (ZSCAN10, SIGLEC14, GHRHR, TBX15, TAS2R1, CDKL1, and CD101) prognostic model for predicting TTR of primary IDH-wt GBM patients using univariate/multivariate Cox regression analyses. The risk scores estimated by the model were significantly negatively correlated with TTR in the training set and two independent testing sets. The model also segregated IDH-wt GBM patients into two groups with significantly divergent progression-free survival outcomes and showed promising performance for predicting 1-, 2-, and 3-year progression-free survival rates in all training and testing sets. Our findings provide new insights into the molecular understanding of GBM progression at recurrence and potential targets for therapeutic treatments.
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Affiliation(s)
- Wei-Min Ho
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
- Ph.D. Program in Translational Medicine, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Department of Neurology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
- College of Medicine, Chang Gung University, Taoyuan, Taiwan
- School of Medicine, National Tsing Hua University, Hsinchu, Taiwan
| | - Chia-Ying Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Tai-Wei Chiang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan
| | - Trees-Juen Chuang
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.
- Ph.D. Program in Translational Medicine, National Taiwan University and Academia Sinica, Taipei, Taiwan.
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13
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Bumbaca B, Birtwistle MR, Gallo JM. Network Analyses of Brain Tumor Patients' Multiomic Data Reveals Pharmacological Opportunities to Alter Cell State Transitions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593202. [PMID: 38766170 PMCID: PMC11100715 DOI: 10.1101/2024.05.08.593202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Glioblastoma Multiforme (GBM) remains a particularly difficult cancer to treat, and survival outcomes remain poor. In addition to the lack of dedicated drug discovery programs for GBM, extensive intratumor heterogeneity and epigenetic plasticity related to cell-state transitions are major roadblocks to successful drug therapy in GBM. To study these phenomenon, publicly available snRNAseq and bulk RNAseq data from patient samples were used to categorize cells from patients into four cell states (i.e. phenotypes), namely: (i) neural progenitor-like (NPC-like), (ii) oligodendrocyte progenitor-like (OPC-like), (iii) astrocyte-like (AC-like), and (iv) mesenchymal-like (MES-like). Patients were subsequently grouped into subpopulations based on which cell-state was the most dominant in their respective tumor. By incorporating phosphoproteomic measurements from the same patients, a protein-protein interaction network (PPIN) was constructed for each cell state. These four-cell state PPINs were pooled to form a single Boolean network that was used for in silico protein knockout simulations to investigate mechanisms that either promote or prevent cell state transitions. Simulation results were input into a boosted tree machine learning model which predicted the cell states or phenotypes of GBM patients from an independent public data source, the Glioma Longitudinal Analysis (GLASS) Consortium. Combining the simulation results and the machine learning predictions, we generated hypotheses for clinically relevant causal mechanisms of cell state transitions. For example, the transcription factor TFAP2A can be seen to promote a transition from the NPC-like to the MES-like state. Such protein nodes and the associated signaling pathways provide potential drug targets that can be further tested in vitro and support cell state-directed (CSD) therapy.
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Affiliation(s)
- Brandon Bumbaca
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo NY, USA
| | - Marc R Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson SC, USA
- Department of Bioengineering, Clemson University, Clemson SC, USA
| | - James M Gallo
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo NY, USA
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14
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Johnson AL, Lopez-Bertoni H. Cellular diversity through space and time: adding new dimensions to GBM therapeutic development. Front Genet 2024; 15:1356611. [PMID: 38774283 PMCID: PMC11106394 DOI: 10.3389/fgene.2024.1356611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/15/2024] [Indexed: 05/24/2024] Open
Abstract
The current median survival for glioblastoma (GBM) patients is only about 16 months, with many patients succumbing to the disease in just a matter of months, making it the most common and aggressive primary brain cancer in adults. This poor outcome is, in part, due to the lack of new treatment options with only one FDA-approved treatment in the last decade. Advances in sequencing techniques and transcriptomic analyses have revealed a vast degree of heterogeneity in GBM, from inter-patient diversity to intra-tumoral cellular variability. These cutting-edge approaches are providing new molecular insights highlighting a critical role for the tumor microenvironment (TME) as a driver of cellular plasticity and phenotypic heterogeneity. With this expanded molecular toolbox, the influence of TME factors, including endogenous (e.g., oxygen and nutrient availability and interactions with non-malignant cells) and iatrogenically induced (e.g., post-therapeutic intervention) stimuli, on tumor cell states can be explored to a greater depth. There exists a critical need for interrogating the temporal and spatial aspects of patient tumors at a high, cell-level resolution to identify therapeutically targetable states, interactions and mechanisms. In this review, we discuss advancements in our understanding of spatiotemporal diversity in GBM with an emphasis on the influence of hypoxia and immune cell interactions on tumor cell heterogeneity. Additionally, we describe specific high-resolution spatially resolved methodologies and their potential to expand the impact of pre-clinical GBM studies. Finally, we highlight clinical attempts at targeting hypoxia- and immune-related mechanisms of malignancy and the potential therapeutic opportunities afforded by single-cell and spatial exploration of GBM patient specimens.
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Affiliation(s)
- Amanda L. Johnson
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Baltimore, MD, United States
| | - Hernando Lopez-Bertoni
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Baltimore, MD, United States
- Oncology, Baltimore, MD, United States
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, MD, United States
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15
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Sloan AR, Silver DJ, Kint S, Gallo M, Lathia JD. Cancer stem cell hypothesis 2.0 in glioblastoma: Where are we now and where are we going? Neuro Oncol 2024; 26:785-795. [PMID: 38394444 PMCID: PMC11066900 DOI: 10.1093/neuonc/noae011] [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] [Indexed: 02/25/2024] Open
Abstract
Over the past 2 decades, the cancer stem cell (CSC) hypothesis has provided insight into many malignant tumors, including glioblastoma (GBM). Cancer stem cells have been identified in patient-derived tumors and in some mouse models, allowing for a deeper understanding of cellular and molecular mechanisms underlying GBM growth and therapeutic resistance. The CSC hypothesis has been the cornerstone of cellular heterogeneity, providing a conceptual and technical framework to explain this longstanding phenotype in GBM. This hypothesis has evolved to fit recent insights into how cellular plasticity drives tumor growth to suggest that CSCs do not represent a distinct population but rather a cellular state with substantial plasticity that can be achieved by non-CSCs under specific conditions. This has further been reinforced by advances in genomics, including single-cell approaches, that have used the CSC hypothesis to identify multiple putative CSC states with unique properties, including specific developmental and metabolic programs. In this review, we provide a historical perspective on the CSC hypothesis and its recent evolution, with a focus on key functional phenotypes, and provide an update on the definition for its use in future genomic studies.
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Affiliation(s)
- Anthony R Sloan
- Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Cleveland, Ohio, USA
| | - Daniel J Silver
- Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Cleveland, Ohio, USA
| | - Sam Kint
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Marco Gallo
- Department of Biochemistry & Molecular Biology, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
- Department of Pediatrics, Section of Hematology and Oncology, Baylor College of Medicine, Houston, Texas, USA
- Texas Children’s Cancer Center, Texas Children’s Hospital, Houston, Texas, USA
| | - Justin D Lathia
- Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA
- Case Comprehensive Cancer Center, Cleveland, Ohio, USA
- Rose Ella Burkhardt Brain Tumor and Neuro-Oncology Center, Cleveland Clinic, Cleveland, Ohio, USA
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16
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Yabo YA, Heiland DH. Understanding glioblastoma at the single-cell level: Recent advances and future challenges. PLoS Biol 2024; 22:e3002640. [PMID: 38814900 PMCID: PMC11139343 DOI: 10.1371/journal.pbio.3002640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024] Open
Abstract
Glioblastoma, the most aggressive and prevalent form of primary brain tumor, is characterized by rapid growth, diffuse infiltration, and resistance to therapies. Intrinsic heterogeneity and cellular plasticity contribute to its rapid progression under therapy; therefore, there is a need to fully understand these tumors at a single-cell level. Over the past decade, single-cell transcriptomics has enabled the molecular characterization of individual cells within glioblastomas, providing previously unattainable insights into the genetic and molecular features that drive tumorigenesis, disease progression, and therapy resistance. However, despite advances in single-cell technologies, challenges such as high costs, complex data analysis and interpretation, and difficulties in translating findings into clinical practice persist. As single-cell technologies are developed further, more insights into the cellular and molecular heterogeneity of glioblastomas are expected, which will help guide the development of personalized and effective therapies, thereby improving prognosis and quality of life for patients.
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Affiliation(s)
- Yahaya A Yabo
- Translational Neurosurgery, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
- Microenvironment and Immunology Research Laboratory, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
| | - Dieter Henrik Heiland
- Translational Neurosurgery, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
- Microenvironment and Immunology Research Laboratory, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
- Department of Neurosurgery, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany
- Department of Neurosurgery, Faculty of Medicine, Medical Center University of Freiburg, Freiburg, Germany
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, Illinois, United States of America
- German Cancer Consortium (DKTK) partner site, Freiburg, Germany
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17
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Yang W, Chen C, Jiang X, Zhao Y, Wang J, Zhang Q, Zhang J, Feng Y, Cui S. CACNA1B protects naked mole-rat hippocampal neuron from apoptosis via altering the subcellular localization of Nrf2 after 60Co irradiation. Cell Biol Int 2024; 48:695-711. [PMID: 38389270 DOI: 10.1002/cbin.12140] [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: 08/26/2022] [Revised: 12/19/2023] [Accepted: 02/01/2024] [Indexed: 02/24/2024]
Abstract
Although radiotherapy is the most effective treatment modality for brain tumors, it always injures the central nervous system, leading to potential sequelae such as cognitive dysfunction. Radiation induces molecular, cellular, and functional changes in neuronal and glial cells. The hippocampus plays a critical role in learning and memory; therefore, concerns about radiation-induced injury are widespread. Multiple studies have focused on this complex problem, but the results have not been fully elucidated. Naked mole rat brains were irradiated with 60Co at a dose of 10 Gy. On 7 days, 14 days, and 28 days after irradiation, hippocampi in the control groups were obtained for next-generation sequencing. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were subsequently performed. Venn diagrams revealed 580 differentially expressed genes (DEGs) that were common at different times after irradiation. GO and KEGG analyses revealed that the 580 common DEGs were enriched in molecular transducer activity. In particular, CACNA1B mediated regulatory effects after irradiation. CACNA1B expression increased significantly after irradiation. Downregulation of CACNA1B led to a reduction in apoptosis and reactive oxygen species levels in hippocampal neurons. This was due to the interaction between CACNA1B and Nrf2, which disturbed the normal nuclear localization of Nrf2. In addition, CACNA1B downregulation led to a decrease in the cognitive functions of naked mole rats. These findings reveal the pivotal role of CACNA1B in regulating radiation-induced brain injury and will lead to the development of a novel strategy to prevent brain injury after irradiation.
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Affiliation(s)
- Wenjing Yang
- Laboratory Animal Science Department, Basic Medical School, Naval Medical University, Shanghai, China
| | - Chao Chen
- Laboratory Animal Science Department, Basic Medical School, Naval Medical University, Shanghai, China
| | - Xiaolong Jiang
- Laboratory Animal Science Department, Basic Medical School, Naval Medical University, Shanghai, China
| | - Yining Zhao
- Clinical Laboratory, Shanghai Yangpu district mental health center, Shanghai University of Medicine and Health Sciences Teaching Hospital, Shanghai, China
| | - Junyang Wang
- Laboratory Animal Science Department, Basic Medical School, Naval Medical University, Shanghai, China
| | - Qianqian Zhang
- Laboratory Animal Science Department, Basic Medical School, Naval Medical University, Shanghai, China
| | - Jingyuan Zhang
- Laboratory Animal Science Department, Basic Medical School, Naval Medical University, Shanghai, China
| | - Yan Feng
- Laboratory Animal Science Department, Basic Medical School, Naval Medical University, Shanghai, China
| | - Shufang Cui
- Laboratory Animal Science Department, Basic Medical School, Naval Medical University, Shanghai, China
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18
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Pichol-Thievend C, Anezo O, Pettiwala AM, Bourmeau G, Montagne R, Lyne AM, Guichet PO, Deshors P, Ballestín A, Blanchard B, Reveilles J, Ravi VM, Joseph K, Heiland DH, Julien B, Leboucher S, Besse L, Legoix P, Dingli F, Liva S, Loew D, Giani E, Ribecco V, Furumaya C, Marcos-Kovandzic L, Masliantsev K, Daubon T, Wang L, Diaz AA, Schnell O, Beck J, Servant N, Karayan-Tapon L, Cavalli FMG, Seano G. VC-resist glioblastoma cell state: vessel co-option as a key driver of chemoradiation resistance. Nat Commun 2024; 15:3602. [PMID: 38684700 PMCID: PMC11058782 DOI: 10.1038/s41467-024-47985-z] [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: 11/10/2023] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Glioblastoma (GBM) is a highly lethal type of cancer. GBM recurrence following chemoradiation is typically attributed to the regrowth of invasive and resistant cells. Therefore, there is a pressing need to gain a deeper understanding of the mechanisms underlying GBM resistance to chemoradiation and its ability to infiltrate. Using a combination of transcriptomic, proteomic, and phosphoproteomic analyses, longitudinal imaging, organotypic cultures, functional assays, animal studies, and clinical data analyses, we demonstrate that chemoradiation and brain vasculature induce cell transition to a functional state named VC-Resist (vessel co-opting and resistant cell state). This cell state is midway along the transcriptomic axis between proneural and mesenchymal GBM cells and is closer to the AC/MES1-like state. VC-Resist GBM cells are highly vessel co-opting, allowing significant infiltration into the surrounding brain tissue and homing to the perivascular niche, which in turn induces even more VC-Resist transition. The molecular and functional characteristics of this FGFR1-YAP1-dependent GBM cell state, including resistance to DNA damage, enrichment in the G2M phase, and induction of senescence/stemness pathways, contribute to its enhanced resistance to chemoradiation. These findings demonstrate how vessel co-option, perivascular niche, and GBM cell plasticity jointly drive resistance to therapy during GBM recurrence.
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Affiliation(s)
- Cathy Pichol-Thievend
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Oceane Anezo
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Aafrin M Pettiwala
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
- Institut Curie, PSL University, 75005, Paris, France
| | - Guillaume Bourmeau
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Remi Montagne
- Institut Curie, PSL University, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- MINES ParisTeach, CBIO-Centre for Computational Biology, PSL Research University, 75006, Paris, France
| | - Anne-Marie Lyne
- Institut Curie, PSL University, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- MINES ParisTeach, CBIO-Centre for Computational Biology, PSL Research University, 75006, Paris, France
| | - Pierre-Olivier Guichet
- Université de Poitiers, CHU Poitiers, ProDiCeT, F-86000, Poitiers, France
- CHU Poitiers, Laboratoire de Cancérologie Biologique, F-86000, Poitiers, France
| | - Pauline Deshors
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Alberto Ballestín
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Benjamin Blanchard
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Juliette Reveilles
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Vidhya M Ravi
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Kevin Joseph
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Dieter H Heiland
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Boris Julien
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | | | - Laetitia Besse
- Institut Curie, PSL University, Université Paris-Saclay, CNRS UMS2016, INSERM US43, Multimodal Imaging Center, 91400, Orsay, France
| | - Patricia Legoix
- Institut Curie, PSL University, ICGex Next-Generation Sequencing Platform, 75005, Paris, France
| | - Florent Dingli
- Institut Curie, PSL University, CurieCoreTech Spectrométrie de Masse Protéomique, 75005, Paris, France
| | - Stephane Liva
- Institut Curie, PSL University, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- MINES ParisTeach, CBIO-Centre for Computational Biology, PSL Research University, 75006, Paris, France
| | - Damarys Loew
- Institut Curie, PSL University, CurieCoreTech Spectrométrie de Masse Protéomique, 75005, Paris, France
| | - Elisa Giani
- Department of Biomedical Sciences, Humanitas University, 20072, Pieve Emanuele, Italy
| | - Valentino Ribecco
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Charita Furumaya
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Laura Marcos-Kovandzic
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France
| | - Konstantin Masliantsev
- Université de Poitiers, CHU Poitiers, ProDiCeT, F-86000, Poitiers, France
- CHU Poitiers, Laboratoire de Cancérologie Biologique, F-86000, Poitiers, France
| | - Thomas Daubon
- Université Bordeaux, CNRS, IBGC, UMR5095, Bordeaux, France
| | - Lin Wang
- Department of Computational and Quantitative Medicine, Hematologic Malignancies Research Institute and Beckman Research Institute, City of Hope, Duarte, CA, USA
| | - Aaron A Diaz
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Oliver Schnell
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Jürgen Beck
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
| | - Nicolas Servant
- Institut Curie, PSL University, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- MINES ParisTeach, CBIO-Centre for Computational Biology, PSL Research University, 75006, Paris, France
| | - Lucie Karayan-Tapon
- Université de Poitiers, CHU Poitiers, ProDiCeT, F-86000, Poitiers, France
- CHU Poitiers, Laboratoire de Cancérologie Biologique, F-86000, Poitiers, France
| | - Florence M G Cavalli
- Institut Curie, PSL University, 75005, Paris, France
- INSERM U900, 75005, Paris, France
- MINES ParisTeach, CBIO-Centre for Computational Biology, PSL Research University, 75006, Paris, France
| | - Giorgio Seano
- Institut Curie, INSERM U1021, CNRS UMR3347, Tumor Microenvironment Lab, Paris-Saclay University, 91400, Orsay, France.
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19
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Yabo YA, Moreno-Sanchez PM, Pires-Afonso Y, Kaoma T, Nosirov B, Scafidi A, Ermini L, Lipsa A, Oudin A, Kyriakis D, Grzyb K, Poovathingal SK, Poli A, Muller A, Toth R, Klink B, Berchem G, Berthold C, Hertel F, Mittelbronn M, Heiland DH, Skupin A, Nazarov PV, Niclou SP, Michelucci A, Golebiewska A. Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts. Genome Med 2024; 16:51. [PMID: 38566128 PMCID: PMC10988817 DOI: 10.1186/s13073-024-01321-8] [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: 12/14/2023] [Accepted: 03/22/2024] [Indexed: 04/04/2024] Open
Abstract
BACKGROUND A major contributing factor to glioblastoma (GBM) development and progression is its ability to evade the immune system by creating an immune-suppressive environment, where GBM-associated myeloid cells, including resident microglia and peripheral monocyte-derived macrophages, play critical pro-tumoral roles. However, it is unclear whether recruited myeloid cells are phenotypically and functionally identical in GBM patients and whether this heterogeneity is recapitulated in patient-derived orthotopic xenografts (PDOXs). A thorough understanding of the GBM ecosystem and its recapitulation in preclinical models is currently missing, leading to inaccurate results and failures of clinical trials. METHODS Here, we report systematic characterization of the tumor microenvironment (TME) in GBM PDOXs and patient tumors at the single-cell and spatial levels. We applied single-cell RNA sequencing, spatial transcriptomics, multicolor flow cytometry, immunohistochemistry, and functional studies to examine the heterogeneous TME instructed by GBM cells. GBM PDOXs representing different tumor phenotypes were compared to glioma mouse GL261 syngeneic model and patient tumors. RESULTS We show that GBM tumor cells reciprocally interact with host cells to create a GBM patient-specific TME in PDOXs. We detected the most prominent transcriptomic adaptations in myeloid cells, with brain-resident microglia representing the main population in the cellular tumor, while peripheral-derived myeloid cells infiltrated the brain at sites of blood-brain barrier disruption. More specifically, we show that GBM-educated microglia undergo transition to diverse phenotypic states across distinct GBM landscapes and tumor niches. GBM-educated microglia subsets display phagocytic and dendritic cell-like gene expression programs. Additionally, we found novel microglial states expressing cell cycle programs, astrocytic or endothelial markers. Lastly, we show that temozolomide treatment leads to transcriptomic plasticity and altered crosstalk between GBM tumor cells and adjacent TME components. CONCLUSIONS Our data provide novel insights into the phenotypic adaptation of the heterogeneous TME instructed by GBM tumors. We show the key role of microglial phenotypic states in supporting GBM tumor growth and response to treatment. Our data place PDOXs as relevant models to assess the functionality of the TME and changes in the GBM ecosystem upon treatment.
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Affiliation(s)
- Yahaya A Yabo
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Pilar M Moreno-Sanchez
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Yolanda Pires-Afonso
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
| | - Tony Kaoma
- Bioinformatics Platform, Department of Medical Informatics, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Bakhtiyor Nosirov
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Andrea Scafidi
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
| | - Luca Ermini
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
| | - Anuja Lipsa
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
| | - Anaïs Oudin
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
| | - Dimitrios Kyriakis
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
| | - Suresh K Poovathingal
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
- Single Cell Analytics & Microfluidics Core, Vlaams Instituut Voor Biotechnologie-KU Leuven, 3000, Louvain, Belgium
| | - Aurélie Poli
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
| | - Arnaud Muller
- Bioinformatics Platform, Department of Medical Informatics, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Reka Toth
- Bioinformatics Platform, Department of Medical Informatics, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Barbara Klink
- National Center of Genetics, Laboratoire National de Santé, L-3555, Dudelange, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
- German Cancer Consortium (DKTK): Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT/UCC), Cancer Consortium (DKTK) Partner Site Dresden, and German Cancer Research Center (DKFZ), Dresden, Heidelberg, 01307, Germany
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307, Dresden, Germany
| | - Guy Berchem
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
- Centre Hospitalier Luxembourg, L-1210, Luxembourg, Luxembourg
| | | | - Frank Hertel
- Centre Hospitalier Luxembourg, L-1210, Luxembourg, Luxembourg
| | - Michel Mittelbronn
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), L-3555, Dudelange, Luxembourg
- National Center of Pathology (NCP), Laboratoire National de Santé, L-3555, Dudelange, Luxembourg
| | - Dieter H Heiland
- Translational Neurosurgery, Friedrich-Alexander University Erlangen Nuremberg, 91054, Erlangen, Germany
- Department of Neurosurgery, University Hospital Erlangen, Friedrich-Alexander University Erlangen Nuremberg, 91054, Erlangen, Germany
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Department of Neurosurgery, Medical Center, University of Freiburg, 79106, Freiburg, Germany
- German Cancer Consortium (DKTK), Partner Site Freiburg, 79106, Freiburg, Germany
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg
- Department of Physics and Material Science, University Luxembourg, L-4367, Belvaux, Luxembourg
- Department of Neuroscience, University of California San Diego, La Jolla, CA, 92093, USA
| | - Petr V Nazarov
- Bioinformatics Platform, Department of Medical Informatics, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445, Strassen, Luxembourg
| | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367, Belvaux, Luxembourg
| | - Alessandro Michelucci
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg.
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1210, Luxembourg, Luxembourg.
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362, Esch-sur-Alzette, Luxembourg.
| | - Anna Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1210, Luxembourg, Luxembourg.
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20
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Marallano VJ, Ughetta ME, Tejero R, Nanda S, Ramalingam R, Stalbow L, Sattiraju A, Huang Y, Ramakrishnan A, Shen L, Wojcinski A, Kesari S, Zou H, Tsankov AM, Friedel RH. Hypoxia drives shared and distinct transcriptomic changes in two invasive glioma stem cell lines. Sci Rep 2024; 14:7246. [PMID: 38538643 PMCID: PMC10973515 DOI: 10.1038/s41598-024-56102-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 03/01/2024] [Indexed: 07/12/2024] Open
Abstract
Glioblastoma (GBM) is the most common primary malignant cancer of the central nervous system. Insufficient oxygenation (hypoxia) has been linked to GBM invasion and aggression, leading to poor patient outcomes. Hypoxia induces gene expression for cellular adaptations. However, GBM is characterized by high intertumoral (molecular subtypes) and intratumoral heterogeneity (cell states), and it is not well understood to what extent hypoxia triggers patient-specific gene responses and cellular diversity in GBM. Here, we surveyed eight patient-derived GBM stem cell lines for invasion phenotypes in 3D culture, which identified two GBM lines showing increased invasiveness in response to hypoxia. RNA-seq analysis of the two patient GBM lines revealed a set of shared hypoxia response genes concerning glucose metabolism, angiogenesis, and autophagy, but also a large set of patient-specific hypoxia-induced genes featuring cell migration and anti-inflammation, highlighting intertumoral diversity of hypoxia responses in GBM. We further applied the Shared GBM Hypoxia gene signature to single cell RNA-seq datasets of glioma patients, which showed that hypoxic cells displayed a shift towards mesenchymal-like (MES) and astrocyte-like (AC) states. Interestingly, in response to hypoxia, tumor cells in IDH-mutant gliomas displayed a strong shift to the AC state, whereas tumor cells in IDH-wildtype gliomas mainly shifted to the MES state. This distinct hypoxia response of IDH-mutant gliomas may contribute to its more favorable prognosis. Our transcriptomic studies provide a basis for future approaches to better understand the diversity of hypoxic niches in gliomas.
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Affiliation(s)
- Valerie J Marallano
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Mary E Ughetta
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rut Tejero
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Sidhanta Nanda
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Rohana Ramalingam
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Lauren Stalbow
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Anirudh Sattiraju
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Yong Huang
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexandre Wojcinski
- Pacific Neuroscience Institute and Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
| | - Santosh Kesari
- Pacific Neuroscience Institute and Saint John's Cancer Institute at Providence Saint John's Health Center, Santa Monica, CA, 90404, USA
| | - Hongyan Zou
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
| | - Roland H Friedel
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.
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21
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Tang W, Lo CWS, Ma W, Chu ATW, Tong AHY, Chung BHY. Revealing the role of SPP1 + macrophages in glioma prognosis and therapeutic targeting by investigating tumor-associated macrophage landscape in grade 2 and 3 gliomas. Cell Biosci 2024; 14:37. [PMID: 38515213 PMCID: PMC10956315 DOI: 10.1186/s13578-024-01218-4] [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: 10/27/2023] [Accepted: 03/13/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Glioma is a highly heterogeneous brain tumor categorized into World Health Organization (WHO) grades 1-4 based on its malignancy. The suppressive immune microenvironment of glioma contributes significantly to unfavourable patient outcomes. However, the cellular composition and their complex interplays within the glioma environment remain poorly understood, and reliable prognostic markers remain elusive. Therefore, in-depth exploration of the tumor microenvironment (TME) and identification of predictive markers are crucial for improving the clinical management of glioma patients. RESULTS Our analysis of single-cell RNA-sequencing data from glioma samples unveiled the immunosuppressive role of tumor-associated macrophages (TAMs), mediated through intricate interactions with tumor cells and lymphocytes. We also discovered the heterogeneity within TAMs, among which a group of suppressive TAMs named TAM-SPP1 demonstrated a significant association with Epidermal Growth Factor Receptor (EGFR) amplification, impaired T cell response and unfavourable patient survival outcomes. Furthermore, by leveraging genomic and transcriptomic data from The Cancer Genome Atlas (TCGA) dataset, two distinct molecular subtypes with a different constitution of TAMs, EGFR status and clinical outcomes were identified. Exploiting the molecular differences between these two subtypes, we developed a four-gene-based prognostic model. This model displayed strong associations with an elevated level of suppressive TAMs and could be used to predict anti-tumor immune response and prognosis in glioma patients. CONCLUSION Our findings illuminated the molecular and cellular mechanisms that shape the immunosuppressive microenvironment in gliomas, providing novel insights into potential therapeutic targets. Furthermore, the developed prognostic model holds promise for predicting immunotherapy response and assisting in more precise risk stratification for glioma patients.
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Affiliation(s)
- Wenshu Tang
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China
| | - Cario W S Lo
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China
| | - Wei Ma
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China
| | - Annie T W Chu
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China
| | - Amy H Y Tong
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China
| | - Brian H Y Chung
- Hong Kong Genome Institute, 2/F, Building 20E, Hong Kong Science Park, Hong Kong, China.
- Department of Pediatrics and Adolescent Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong, China.
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22
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Shi H, Williams MJ, Satas G, Weiner AC, McPherson A, Shah SP. Allele-specific transcriptional effects of subclonal copy number alterations enable genotype-phenotype mapping in cancer cells. Nat Commun 2024; 15:2482. [PMID: 38509111 PMCID: PMC10954741 DOI: 10.1038/s41467-024-46710-0] [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: 01/18/2023] [Accepted: 03/01/2024] [Indexed: 03/22/2024] Open
Abstract
Subclonal copy number alterations are a prevalent feature in tumors with high chromosomal instability and result in heterogeneous cancer cell populations with distinct phenotypes. However, the extent to which subclonal copy number alterations contribute to clone-specific phenotypes remains poorly understood. We develop TreeAlign, which computationally integrates independently sampled single-cell DNA and RNA sequencing data from the same cell population. TreeAlign accurately encodes dosage effects from subclonal copy number alterations, the impact of allelic imbalance on allele-specific transcription, and obviates the need to define genotypic clones from a phylogeny a priori, leading to highly granular definitions of clones with distinct expression programs. These improvements enable clone-clone gene expression comparisons with higher resolution and identification of expression programs that are genomically independent. Our approach sets the stage for dissecting the relative contribution of fixed genomic alterations and dynamic epigenetic processes on gene expression programs in cancer.
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Affiliation(s)
- Hongyu Shi
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY, USA
| | - Marc J Williams
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Gryte Satas
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Adam C Weiner
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
- Tri-Institutional PhD Program in Computational Biology and Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Andrew McPherson
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Sohrab P Shah
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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23
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Xie D, Huang H, Guo Y, Jiang Z, Kuang Y, Huang H, Liu W, Wang L, Xin Z, Wang B, Ren C, Jiang X. Integrated profiling identifies ferredoxin 1 as an immune-related biomarker of malignant phenotype in glioma. Heliyon 2024; 10:e26976. [PMID: 38463788 PMCID: PMC10923675 DOI: 10.1016/j.heliyon.2024.e26976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/18/2024] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Background Glioma, a highly resistant and recurrent type of central nervous system tumor, poses a significant challenge in terms of effective drug treatments and its associated mortality rates. Despite the discovery of Ferredoxin 1 (FDX1) as a crucial participant in cuproptosis, an innovative mechanism of cellular demise, its precise implications for glioma prognosis and tumor immune infiltration remain inadequately elucidated. Methods To analyze pan-cancer data, we employed multiple public databases. Gene expression evaluation was performed using tissue microarray (TMA) and single-cell sequencing data. Furthermore, four different approaches were employed to assess the prognostic importance of FDX1 in glioma. We conducted the analysis of differential expression genes (DEGs) and Gene Set Enrichment Analysis (GSEA) to identify immune-related predictive signaling pathways. Somatic mutations were assessed using Tumor Mutation Burden (TMB) and waterfall plots. Immune cell infiltration was evaluated with five different algorithms. Furthermore, we performed in vitro investigations to evaluate the biological roles of FDX1 in glioma. Results Glioma samples exhibited upregulation of FDX1, which in turn predicted poor prognosis and was positively associated with unfavorable clinicopathological characteristics. Notably, the top four enriched signaling pathways were immune-related, and the discovery revealed a connection between the expression of FDX1 and the frequency of mutations or the TMB. The FDX1_high group exhibited heightened infiltration of immune cells, and there existed a direct association between the expression of FDX1 and the regulation of immune checkpoint. In vitro experiments demonstrated that FDX1 knockdown reduced proliferation, migration, invasion and transition from G2 to M phase in glioma cells. Conclusion In glioma, FDX1 demonstrated a positive association with the advancement of malignancy and changes in the infiltration of immune cells.
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Affiliation(s)
- Dongcheng Xie
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Hailong Huang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Youwei Guo
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Zhipeng Jiang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yirui Kuang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Haoxuan Huang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Weidong Liu
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
- The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Lei Wang
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
- The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Zhaoqi Xin
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Binbin Wang
- Department of Neurosurgery, The First Affiliated Hospital with Nanjing Medical University, 300 Guangzhou Road, Nanjing, China
| | - Caiping Ren
- Cancer Research Institute, School of Basic Medical Science, Central South University, Changsha, China
- The NHC Key Laboratory of Carcinogenesis and The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Central South University, Changsha, China
| | - Xingjun Jiang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
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24
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Lan Z, Li X, Zhang X. Glioblastoma: An Update in Pathology, Molecular Mechanisms and Biomarkers. Int J Mol Sci 2024; 25:3040. [PMID: 38474286 PMCID: PMC10931698 DOI: 10.3390/ijms25053040] [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: 02/01/2024] [Revised: 02/28/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
Glioblastoma multiforme (GBM) is the most common and malignant type of primary brain tumor in adults. Despite important advances in understanding the molecular pathogenesis and biology of this tumor in the past decade, the prognosis for GBM patients remains poor. GBM is characterized by aggressive biological behavior and high degrees of inter-tumor and intra-tumor heterogeneity. Increased understanding of the molecular and cellular heterogeneity of GBM may not only help more accurately define specific subgroups for precise diagnosis but also lay the groundwork for the successful implementation of targeted therapy. Herein, we systematically review the key achievements in the understanding of GBM molecular pathogenesis, mechanisms, and biomarkers in the past decade. We discuss the advances in the molecular pathology of GBM, including genetics, epigenetics, transcriptomics, and signaling pathways. We also review the molecular biomarkers that have potential clinical roles. Finally, new strategies, current challenges, and future directions for discovering new biomarkers and therapeutic targets for GBM will be discussed.
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Affiliation(s)
| | | | - Xiaoqin Zhang
- Department of Pathology, School of Medicine, South China University of Technology, Guangzhou 510006, China; (Z.L.); (X.L.)
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25
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Zhang W, Dang R, Liu H, Dai L, Liu H, Adegboro AA, Zhang Y, Li W, Peng K, Hong J, Li X. Machine learning-based investigation of regulated cell death for predicting prognosis and immunotherapy response in glioma patients. Sci Rep 2024; 14:4173. [PMID: 38378721 PMCID: PMC10879095 DOI: 10.1038/s41598-024-54643-3] [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: 12/06/2023] [Accepted: 02/14/2024] [Indexed: 02/22/2024] Open
Abstract
Glioblastoma is a highly aggressive and malignant type of brain cancer that originates from glial cells in the brain, with a median survival time of 15 months and a 5-year survival rate of less than 5%. Regulated cell death (RCD) is the autonomous and orderly cell death under genetic control, controlled by precise signaling pathways and molecularly defined effector mechanisms, modulated by pharmacological or genetic interventions, and plays a key role in maintaining homeostasis of the internal environment. The comprehensive and systemic landscape of the RCD in glioma is not fully investigated and explored. After collecting 18 RCD-related signatures from the opening literature, we comprehensively explored the RCD landscape, integrating the multi-omics data, including large-scale bulk data, single-cell level data, glioma cell lines, and proteome level data. We also provided a machine learning framework for screening the potentially therapeutic candidates. Here, based on bulk and single-cell sequencing samples, we explored RCD-related phenotypes, investigated the profile of the RCD, and developed an RCD gene pair scoring system, named RCD.GP signature, showing a reliable and robust performance in predicting the prognosis of glioblastoma. Using the machine learning framework consisting of Lasso, RSF, XgBoost, Enet, CoxBoost and Boruta, we identified seven RCD genes as potential therapeutic targets in glioma and verified that the SLC43A3 highly expressed in glioma grades and glioma cell lines through qRT-PCR. Our study provided comprehensive insights into the RCD roles in glioma, developed a robust RCD gene pair signature for predicting the prognosis of glioma patients, constructed a machine learning framework for screening the core candidates and identified the SLC43A3 as an oncogenic role and a prediction biomarker in glioblastoma.
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Affiliation(s)
- Wei Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Ruiyue Dang
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China
| | - Hongyi Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Luohuan Dai
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Hongwei Liu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Abraham Ayodeji Adegboro
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Yihao Zhang
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Wang Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
| | - Kang Peng
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China
- Department of Radiology, Xiangya Hospital, Central South University, Changsha, China
| | - Jidong Hong
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, China.
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, China.
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26
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Fu Z, Chen Z, Ye J, Ji J, Ni W, Lin W, Lin H, Lu L, Zhu G, Xie Q, Yan F, Chen G, Liu F. Identifying PLAUR as a Pivotal Gene of Tumor Microenvironment and Regulating Mesenchymal Phenotype of Glioblastoma. Cancers (Basel) 2024; 16:840. [PMID: 38398231 PMCID: PMC10887327 DOI: 10.3390/cancers16040840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/04/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
The mesenchymal (MES) phenotype of glioblastoma (GBM) is the most aggressive and therapy-resistant subtype of GBM. The MES phenotype transition during tumor progression results from both tumor-intrinsic genetic alterations and tumor-extrinsic microenvironmental factors. In this study, we sought to identify genes that can modulate the MES phenotype via both mechanisms. By integrating weighted gene co-expression network analysis (WGCNA) and the differential expression analysis of hypoxia-immunosuppression-related genes, we identified the plasminogen activator, urokinase receptor (PLAUR) as the hub gene. Functional enrichment analysis and GSVA analysis demonstrated that PLAUR was associated with the MES phenotype of glioma and the hypoxia-immunosuppression-related microenvironmental components. Single-cell sequencing analysis revealed that PLAUR mediated the ligand-receptor interaction between tumor-associated macrophages (TAMs) and glioma cells. Functional experiments in vitro with cell lines or primary glioma cells and xenograft models using BALB/c nude mice confirmed the role of PLAUR in promoting the MES phenotype of GBM. Our findings indicate that PLAUR regulates both glioma cells and tumor cell-extrinsic factors that favor the MES phenotype and suggest that PLAUR might be a potential target for GBM therapy.
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Affiliation(s)
- Zaixiang Fu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, China; (Z.F.); (Z.C.); (J.Y.); (J.J.); (W.N.); (W.L.); (H.L.); (L.L.); (Q.X.); (F.Y.)
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou 310000, China
| | - Zihang Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, China; (Z.F.); (Z.C.); (J.Y.); (J.J.); (W.N.); (W.L.); (H.L.); (L.L.); (Q.X.); (F.Y.)
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou 310000, China
| | - Jingya Ye
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, China; (Z.F.); (Z.C.); (J.Y.); (J.J.); (W.N.); (W.L.); (H.L.); (L.L.); (Q.X.); (F.Y.)
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou 310000, China
| | - Jianxiong Ji
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, China; (Z.F.); (Z.C.); (J.Y.); (J.J.); (W.N.); (W.L.); (H.L.); (L.L.); (Q.X.); (F.Y.)
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou 310000, China
| | - Weifang Ni
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, China; (Z.F.); (Z.C.); (J.Y.); (J.J.); (W.N.); (W.L.); (H.L.); (L.L.); (Q.X.); (F.Y.)
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou 310000, China
| | - Weibo Lin
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, China; (Z.F.); (Z.C.); (J.Y.); (J.J.); (W.N.); (W.L.); (H.L.); (L.L.); (Q.X.); (F.Y.)
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou 310000, China
| | - Haopu Lin
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, China; (Z.F.); (Z.C.); (J.Y.); (J.J.); (W.N.); (W.L.); (H.L.); (L.L.); (Q.X.); (F.Y.)
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou 310000, China
| | - Liquan Lu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, China; (Z.F.); (Z.C.); (J.Y.); (J.J.); (W.N.); (W.L.); (H.L.); (L.L.); (Q.X.); (F.Y.)
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou 310000, China
| | - Ganggui Zhu
- Department of Lung Transplantation, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310052, China;
| | - Qin Xie
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, China; (Z.F.); (Z.C.); (J.Y.); (J.J.); (W.N.); (W.L.); (H.L.); (L.L.); (Q.X.); (F.Y.)
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou 310000, China
| | - Feng Yan
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, China; (Z.F.); (Z.C.); (J.Y.); (J.J.); (W.N.); (W.L.); (H.L.); (L.L.); (Q.X.); (F.Y.)
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou 310000, China
| | - Gao Chen
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, China; (Z.F.); (Z.C.); (J.Y.); (J.J.); (W.N.); (W.L.); (H.L.); (L.L.); (Q.X.); (F.Y.)
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou 310000, China
| | - Fuyi Liu
- Department of Neurosurgery, The Second Affiliated Hospital of Zhejiang University School of Medicine, Hangzhou 310000, China; (Z.F.); (Z.C.); (J.Y.); (J.J.); (W.N.); (W.L.); (H.L.); (L.L.); (Q.X.); (F.Y.)
- Key Laboratory of Precise Treatment and Clinical Translational Research of Neurological Diseases, Hangzhou 310000, China
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27
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Galbo PM, Madsen AT, Liu Y, Peng M, Wei Y, Ciesielski MJ, Fenstermaker RA, Graff S, Montagna C, Segall JE, Sidoli S, Zang X, Zheng D. Functional Contribution and Clinical Implication of Cancer-Associated Fibroblasts in Glioblastoma. Clin Cancer Res 2024; 30:865-876. [PMID: 38060213 PMCID: PMC10922678 DOI: 10.1158/1078-0432.ccr-23-0493] [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: 02/16/2023] [Revised: 05/11/2023] [Accepted: 12/05/2023] [Indexed: 12/08/2023]
Abstract
PURPOSE The abundance and biological contribution of cancer-associated fibroblasts (CAF) in glioblastoma (GBM) are poorly understood. Here, we aim to uncover its molecular signature, cellular roles, and potential tumorigenesis implications. EXPERIMENTAL DESIGN We first applied single-cell RNA sequencing (RNA-seq) and bioinformatics analysis to identify and characterize stromal cells with CAF transcriptomic features in human GBM tumors. Then, we performed functional enrichment analysis and in vitro assays to investigate their interactions with malignant GBM cells. RESULTS We found that CAF abundance was low but significantly correlated with tumor grade, poor clinical outcome, and activation of extracellular matrix remodeling using three large cohorts containing bulk RNA-seq data and clinical information. Proteomic analysis of a GBM-derived CAF line and its secretome revealed fibronectin (FN1) as a critical candidate factor mediating CAF functions. This was validated using in vitro cellular models, which demonstrated that CAF-conditioned media and recombinant FN1 could facilitate the migration and invasion of GBM cells. In addition, we showed that CAFs were more abundant in the mesenchymal-like state (or subtype) than in other states of GBMs. Interestingly, cell lines resembling the proneural state responded to the CAF signaling better for the migratory and invasive phenotypes. CONCLUSIONS Overall, this study characterized the molecular features and functional impacts of CAFs in GBM, alluding to novel cell interactions mediated by CAFs in the GBM microenvironment.
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Affiliation(s)
- Phillip M. Galbo
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York
| | - Anne Tranberg Madsen
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York
| | - Yang Liu
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
| | - Mou Peng
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York
| | - Yao Wei
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York
| | - Michael J Ciesielski
- Department of Neurosurgery, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | - Sarah Graff
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York
| | - Cristina Montagna
- Department of Radiation Oncology, Rutgers University, New Brunswick, New Jersey
| | - Jeffrey E. Segall
- Department of Pathology, Albert Einstein College of Medicine, Bronx, New York
| | - Simone Sidoli
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, New York
| | - Xingxing Zang
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York
- Department of Medicine, Albert Einstein College of Medicine, Bronx, New York
- Department of Urology, Albert Einstein College of Medicine, Bronx, New York
| | - Deyou Zheng
- Department of Genetics, Albert Einstein College of Medicine, Bronx, New York
- Departments of Neurology and Neuroscience, Albert Einstein College of Medicine, Bronx, New York
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28
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Tanner G, Barrow R, Ajaib S, Al-Jabri M, Ahmed N, Pollock S, Finetti M, Rippaus N, Bruns AF, Syed K, Poulter JA, Matthews L, Hughes T, Wilson E, Johnson C, Varn FS, Brüning-Richardson A, Hogg C, Droop A, Gusnanto A, Care MA, Cutillo L, Westhead DR, Short SC, Jenkinson MD, Brodbelt A, Chakrabarty A, Ismail A, Verhaak RGW, Stead LF. IDHwt glioblastomas can be stratified by their transcriptional response to standard treatment, with implications for targeted therapy. Genome Biol 2024; 25:45. [PMID: 38326875 PMCID: PMC10848526 DOI: 10.1186/s13059-024-03172-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 01/11/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Glioblastoma (GBM) brain tumors lacking IDH1 mutations (IDHwt) have the worst prognosis of all brain neoplasms. Patients receive surgery and chemoradiotherapy but tumors almost always fatally recur. RESULTS Using RNA sequencing data from 107 pairs of pre- and post-standard treatment locally recurrent IDHwt GBM tumors, we identify two responder subtypes based on longitudinal changes in gene expression. In two thirds of patients, a specific subset of genes is upregulated from primary to recurrence (Up responders), and in one third, the same genes are downregulated (Down responders), specifically in neoplastic cells. Characterization of the responder subtypes indicates subtype-specific adaptive treatment resistance mechanisms that are associated with distinct changes in the tumor microenvironment. In Up responders, recurrent tumors are enriched in quiescent proneural GBM stem cells and differentiated neoplastic cells, with increased interaction with the surrounding normal brain and neurotransmitter signaling, whereas Down responders commonly undergo mesenchymal transition. ChIP-sequencing data from longitudinal GBM tumors suggests that the observed transcriptional reprogramming could be driven by Polycomb-based chromatin remodeling rather than DNA methylation. CONCLUSIONS We show that the responder subtype is cancer-cell intrinsic, recapitulated in in vitro GBM cell models, and influenced by the presence of the tumor microenvironment. Stratifying GBM tumors by responder subtype may lead to more effective treatment.
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Affiliation(s)
- Georgette Tanner
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Rhiannon Barrow
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Shoaib Ajaib
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Muna Al-Jabri
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Nazia Ahmed
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Steven Pollock
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Martina Finetti
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Nora Rippaus
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Alexander F Bruns
- Leeds Institute of Cardiovascular and Metabolic Medicine, University of Leeds, Leeds, UK
| | - Khaja Syed
- The Walton Centre NHS Foundation Trust, Liverpool, UK
| | - James A Poulter
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Laura Matthews
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Thomas Hughes
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
- School of Science, Technology and Health, York St John University, York, YO31 7EX, UK
| | - Erica Wilson
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Colin Johnson
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Frederick S Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Catherine Hogg
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | | | | | - Matthew A Care
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
| | - Luisa Cutillo
- School of Mathematics, University of Leeds, Leeds, UK
| | - David R Westhead
- School of Molecular and Cellular Biology, University of Leeds, Leeds, UK
| | - Susan C Short
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK
- Leeds Teaching Hospital, Leeds, UK
| | - Michael D Jenkinson
- The Walton Centre NHS Foundation Trust, Liverpool, UK
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | | | | | | | - Roel G W Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Yale School of Medicine, New Haven, CT, USA
| | - Lucy F Stead
- Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK.
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29
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Wang C, Sun M, Shao C, Schlicker L, Zhuo Y, Harim Y, Peng T, Tian W, Stöffler N, Schneider M, Helm D, Chu Y, Fu B, Jin X, Mallm JP, Mall M, Wu Y, Schulze A, Liu HK. A multidimensional atlas of human glioblastoma-like organoids reveals highly coordinated molecular networks and effective drugs. NPJ Precis Oncol 2024; 8:19. [PMID: 38273014 PMCID: PMC10811239 DOI: 10.1038/s41698-024-00500-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 01/04/2024] [Indexed: 01/27/2024] Open
Abstract
Recent advances in the genomics of glioblastoma (GBM) led to the introduction of molecular neuropathology but failed to translate into treatment improvement. This is largely attributed to the genetic and phenotypic heterogeneity of GBM, which are considered the major obstacle to GBM therapy. Here, we use advanced human GBM-like organoid (LEGO: Laboratory Engineered Glioblastoma-like Organoid) models and provide an unprecedented comprehensive characterization of LEGO models using single-cell transcriptome, DNA methylome, metabolome, lipidome, proteome, and phospho-proteome analysis. We discovered that genetic heterogeneity dictates functional heterogeneity across molecular layers and demonstrates that NF1 mutation drives mesenchymal signature. Most importantly, we found that glycerol lipid reprogramming is a hallmark of GBM, and several targets and drugs were discovered along this line. We also provide a genotype-based drug reference map using LEGO-based drug screen. This study provides new human GBM models and a research path toward effective GBM therapy.
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Affiliation(s)
- Changwen Wang
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ); The DKFZ-ZMBH alliance, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.
- Faculty of Medicine, Heidelberg University, Im Neuenheimer Feld 672, 69120, Heidelberg, Germany.
- Department of Thyroid Surgery, The First Affiliated Hospital, School of Medicine, Zhejiang University, 310003, Hangzhou, China.
| | - Meng Sun
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Chunxuan Shao
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ); The DKFZ-ZMBH alliance, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Lisa Schlicker
- Division of Tumor Metabolism and Microenvironment, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Yue Zhuo
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ); The DKFZ-ZMBH alliance, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Yassin Harim
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ); The DKFZ-ZMBH alliance, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Im Neuenheimer Feld 234, 69120, Heidelberg, Germany
| | - Tianping Peng
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Weili Tian
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ); The DKFZ-ZMBH alliance, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Nadja Stöffler
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ); The DKFZ-ZMBH alliance, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Martin Schneider
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Dominic Helm
- Proteomics Core Facility, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany
| | - Youjun Chu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Beibei Fu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
- School of Life Science and Technology, ShanghaiTech University, 201210, Shanghai, China
| | - Xiaoliang Jin
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China
- Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, 200025, Shanghai, China
| | - Jan-Philipp Mallm
- Single-cell Open Lab, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Moritz Mall
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, 69120, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, 68159, Mannheim, Germany
| | - Yonghe Wu
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China
| | - Almut Schulze
- Division of Tumor Metabolism and Microenvironment, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 581, 69120, Heidelberg, Germany
| | - Hai-Kun Liu
- Division of Molecular Neurogenetics, German Cancer Research Center (DKFZ); The DKFZ-ZMBH alliance, Im Neuenheimer Feld 581, 69120, Heidelberg, Germany.
- Shanghai Institute for Advanced Immunochemical Studies, ShanghaiTech University, 201210, Shanghai, China.
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30
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Drexler R, Khatri R, Schüller U, Eckhardt A, Ryba A, Sauvigny T, Dührsen L, Mohme M, Ricklefs T, Bode H, Hausmann F, Huber TB, Bonn S, Voß H, Neumann JE, Silverbush D, Hovestadt V, Suvà ML, Lamszus K, Gempt J, Westphal M, Heiland DH, Hänzelmann S, Ricklefs FL. Temporal change of DNA methylation subclasses between matched newly diagnosed and recurrent glioblastoma. Acta Neuropathol 2024; 147:21. [PMID: 38244080 PMCID: PMC10799798 DOI: 10.1007/s00401-023-02677-8] [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: 09/14/2023] [Revised: 12/08/2023] [Accepted: 12/24/2023] [Indexed: 01/22/2024]
Abstract
The longitudinal transition of phenotypes is pivotal in glioblastoma treatment resistance and DNA methylation emerged as an important tool for classifying glioblastoma phenotypes. We aimed to characterize DNA methylation subclass heterogeneity during progression and assess its clinical impact. Matched tissues from 47 glioblastoma patients were subjected to DNA methylation profiling, including CpG-site alterations, tissue and serum deconvolution, mass spectrometry, and immunoassay. Effects of clinical characteristics on temporal changes and outcomes were studied. Among 47 patients, 8 (17.0%) had non-matching classifications at recurrence. In the remaining 39 cases, 28.2% showed dominant DNA methylation subclass transitions, with 72.7% being a mesenchymal subclass. In general, glioblastomas with a subclass transition showed upregulated metabolic processes. Newly diagnosed glioblastomas with mesenchymal transition displayed increased stem cell-like states and decreased immune components at diagnosis and exhibited elevated immune signatures and cytokine levels in serum. In contrast, tissue of recurrent glioblastomas with mesenchymal transition showed increased immune components but decreased stem cell-like states. Survival analyses revealed comparable outcomes for patients with and without subclass transitions. This study demonstrates a temporal heterogeneity of DNA methylation subclasses in 28.2% of glioblastomas, not impacting patient survival. Changes in cell state composition associated with subclass transition may be crucial for recurrent glioblastoma targeted therapies.
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Affiliation(s)
- Richard Drexler
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Robin Khatri
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, Research Institute Children's Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Alicia Eckhardt
- Department of Pediatric Hematology and Oncology, Research Institute Children's Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Department of Radiation Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alice Ryba
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Thomas Sauvigny
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Lasse Dührsen
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Malte Mohme
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Tammo Ricklefs
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Helena Bode
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Fabian Hausmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hannah Voß
- Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia E Neumann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dana Silverbush
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Volker Hovestadt
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mario L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Jens Gempt
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Dieter H Heiland
- Department of Neurosurgery, Medical Center University of Freiburg, Freiburg, Germany
| | - Sonja Hänzelmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Franz L Ricklefs
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
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Mathur R, Wang Q, Schupp PG, Nikolic A, Hilz S, Hong C, Grishanina NR, Kwok D, Stevers NO, Jin Q, Youngblood MW, Stasiak LA, Hou Y, Wang J, Yamaguchi TN, Lafontaine M, Shai A, Smirnov IV, Solomon DA, Chang SM, Hervey-Jumper SL, Berger MS, Lupo JM, Okada H, Phillips JJ, Boutros PC, Gallo M, Oldham MC, Yue F, Costello JF. Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective. Cell 2024; 187:446-463.e16. [PMID: 38242087 PMCID: PMC10832360 DOI: 10.1016/j.cell.2023.12.013] [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: 04/06/2023] [Revised: 10/03/2023] [Accepted: 12/06/2023] [Indexed: 01/21/2024]
Abstract
Treatment failure for the lethal brain tumor glioblastoma (GBM) is attributed to intratumoral heterogeneity and tumor evolution. We utilized 3D neuronavigation during surgical resection to acquire samples representing the whole tumor mapped by 3D spatial coordinates. Integrative tissue and single-cell analysis revealed sources of genomic, epigenomic, and microenvironmental intratumoral heterogeneity and their spatial patterning. By distinguishing tumor-wide molecular features from those with regional specificity, we inferred GBM evolutionary trajectories from neurodevelopmental lineage origins and initiating events such as chromothripsis to emergence of genetic subclones and spatially restricted activation of differential tumor and microenvironmental programs in the core, periphery, and contrast-enhancing regions. Our work depicts GBM evolution and heterogeneity from a 3D whole-tumor perspective, highlights potential therapeutic targets that might circumvent heterogeneity-related failures, and establishes an interactive platform enabling 360° visualization and analysis of 3D spatial patterns for user-selected genes, programs, and other features across whole GBM tumors.
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Affiliation(s)
- Radhika Mathur
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Qixuan Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Patrick G Schupp
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Ana Nikolic
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB
| | - Stephanie Hilz
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Chibo Hong
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nadia R Grishanina
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Darwin Kwok
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Nicholas O Stevers
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Qiushi Jin
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Mark W Youngblood
- Department of Neurological Surgery, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Lena Ann Stasiak
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ye Hou
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Juan Wang
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Takafumi N Yamaguchi
- Department of Human Genetics, University of California, Los Angeles, Los Angees, CA, USA
| | - Marisa Lafontaine
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Ivan V Smirnov
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - David A Solomon
- Department of Pathology, University of California San Francisco, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Janine M Lupo
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Hideho Okada
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Paul C Boutros
- Department of Human Genetics, University of California, Los Angeles, Los Angees, CA, USA
| | - Marco Gallo
- Department of Biochemistry & Molecular Biology, University of Calgary, Calgary, AB; Department of Pediatrics, Baylor College of Medicine, Texas Children's Hospital, Houston, TX, USA
| | - Michael C Oldham
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA
| | - Feng Yue
- Department of Biochemistry and Molecular Genetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA; Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, USA.
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32
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Bahcheli AT, Min HK, Bayati M, Zhao H, Fortuna A, Dong W, Dzneladze I, Chan J, Chen X, Guevara-Hoyer K, Dirks PB, Huang X, Reimand J. Pan-cancer ion transport signature reveals functional regulators of glioblastoma aggression. EMBO J 2024; 43:196-224. [PMID: 38177502 PMCID: PMC10897389 DOI: 10.1038/s44318-023-00016-x] [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: 05/05/2023] [Revised: 11/30/2023] [Accepted: 11/30/2023] [Indexed: 01/06/2024] Open
Abstract
Ion channels, transporters, and other ion-flux controlling proteins, collectively comprising the "ion permeome", are common drug targets, however, their roles in cancer remain understudied. Our integrative pan-cancer transcriptome analysis shows that genes encoding the ion permeome are significantly more often highly expressed in specific subsets of cancer samples, compared to pan-transcriptome expectations. To enable target selection, we identified 410 survival-associated IP genes in 33 cancer types using a machine-learning approach. Notably, GJB2 and SCN9A show prominent expression in neoplastic cells and are associated with poor prognosis in glioblastoma, the most common and aggressive brain cancer. GJB2 or SCN9A knockdown in patient-derived glioblastoma cells induces transcriptome-wide changes involving neuron projection and proliferation pathways, impairs cell viability and tumor sphere formation in vitro, perturbs tunneling nanotube dynamics, and extends the survival of glioblastoma-bearing mice. Thus, aberrant activation of genes encoding ion transport proteins appears as a pan-cancer feature defining tumor heterogeneity, which can be exploited for mechanistic insights and therapy development.
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Affiliation(s)
- Alexander T Bahcheli
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Hyun-Kee Min
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Masroor Bayati
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Hongyu Zhao
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Department of Neurosurgery and Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Alexander Fortuna
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Weifan Dong
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Irakli Dzneladze
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Jade Chan
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Xin Chen
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
- Songjiang Research Institute, Songjiang Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Kissy Guevara-Hoyer
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada
- Cancer Immunomonitoring and Immuno-Mediated Pathologies Support Unit, Department of Clinical Immunology, Institute of Laboratory Medicine (IML) and Biomedical Research Foundation (IdiSCC), San Carlos Clinical Hospital, Madrid, Spain
| | - Peter B Dirks
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada
| | - Xi Huang
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Developmental and Stem Cell Biology Program, The Hospital for Sick Children, Toronto, ON, Canada.
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, ON, Canada.
| | - Jüri Reimand
- Computational Biology Program, Ontario Institute for Cancer Research, Toronto, ON, Canada.
- Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
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33
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Jain R, Krishnan S, Lee S, Amoozgar Z, Subudhi S, Kumar A, Posada J, Lindeman N, Lei P, Duquette M, Roberge S, Huang P, Andersson P, Datta M, Munn L, Fukumura D. Wnt inhibition alleviates resistance to immune checkpoint blockade in glioblastoma. RESEARCH SQUARE 2023:rs.3.rs-3707472. [PMID: 38234841 PMCID: PMC10793505 DOI: 10.21203/rs.3.rs-3707472/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Wnt signaling plays a critical role in the progression and treatment outcome of glioblastoma (GBM). Here, we identified WNT7b as a heretofore unknown mechanism of resistance to immune checkpoint inhibition (αPD1) in GBM patients and murine models. Acquired resistance to αPD1 was found to be associated with the upregulation of Wnt7b and β-catenin protein levels in GBM in patients and in a clinically relevant, stem-rich GBM model. Combining the porcupine inhibitor WNT974 with αPD1 prolonged the survival of GBM-bearing mice. However, this combination had a dichotomous response, with a subset of tumors showing refractoriness. WNT974 and αPD1 expanded a subset of DC3-like dendritic cells (DCs) and decreased the granulocytic myeloid-derived suppressor cells (gMDSCs) in the tumor microenvironment (TME). By contrast, monocytic MDSCs (mMDSCs) increased, while T-cell infiltration remained unchanged, suggesting potential TME-mediated resistance. Our preclinical findings warrant the testing of Wnt7b/β-catenin combined with αPD1 in GBM patients with elevated Wnt7b/β-catenin signaling.
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Gao M, Huang J, Yang B, Liu Q, Luo M, Yang B, Li X, Liu X. Identification of efferocytosis-related subtypes in gliomas and elucidating their characteristics and clinical significance. Front Cell Dev Biol 2023; 11:1295891. [PMID: 38161335 PMCID: PMC10757721 DOI: 10.3389/fcell.2023.1295891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024] Open
Abstract
Introduction: Gliomas, the most prevalent tumors of the central nervous system, are known for their aggressive nature and poor prognosis. The heterogeneity among gliomas leads to varying responses to the same treatments, even among similar glioma types. In our study, we efferocytosis-related subtypes and explored their characteristics in terms of immune landscape, intercellular communication, and metabolic processes, ultimately elucidating their potential clinical implications. Methods and Results: We first identified efferocytosis-related subtypes in Bulk RNA-seq using the NMF algorithm. We then preliminarily demonstrated the correlation of these subtypes with efferocytosis by examining enrichment scores of cell death pathways, macrophage infiltration, and the expression of immune ligands. Our analysis of single-cell RNA-seq data further supported the association of these subtypes with efferocytosis. Through enrichment analysis, we found that efferocytosis-related subtypes differ from other types of gliomas in terms of immune landscape, intercellular communication, and substance metabolism. Moreover, we found that the efferocytosis-related classification is a prognostic factor with robust predictive performance by calculating the AUC values. We also found that efferocytosis-related subtypes, when compared with other gliomas in drug sensitivity, survival, and TIDE scores, show a clear link to the effectiveness of chemotherapy, radiotherapy, and immunotherapy in glioma patients. Discussion: We identified efferocytosis-related subtypes in gliomas by analyzing the expression of 137 efferocytosis-associated genes, exploring their characteristics in immune landscape, intercellular communication, metabolic processes, and genomic variations. Moreover, we discovered that the classification of efferocytosis-related subtypes has a strong prognostic predictive power and holds potential significance in guiding clinical treatment.
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Affiliation(s)
- Mengge Gao
- Department of Clinical Nutrition, Huadu District People’s Hospital of Guangzhou, Southern Medical University, Guangzhou, China
| | - Jinsheng Huang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Bo Yang
- Department of Clinical Nutrition, Huadu District People’s Hospital of Guangzhou, Southern Medical University, Guangzhou, China
| | - Qiong Liu
- Department of Clinical Nutrition, Huadu District People’s Hospital of Guangzhou, Southern Medical University, Guangzhou, China
| | - Miaoqing Luo
- Department of Clinical Nutrition, Huadu District People’s Hospital of Guangzhou, Southern Medical University, Guangzhou, China
| | - Biying Yang
- Department of Clinical Nutrition, Huadu District People’s Hospital of Guangzhou, Southern Medical University, Guangzhou, China
| | - Xujia Li
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Xiaofang Liu
- Department of Clinical Nutrition, Huadu District People’s Hospital of Guangzhou, Southern Medical University, Guangzhou, China
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35
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Brynjulvsen M, Solli E, Walewska M, Zucknick M, Djirackor L, Langmoen IA, Mughal AA, Skaga E, Vik-Mo EO, Sandberg CJ. Functional and Molecular Heterogeneity in Glioma Stem Cells Derived from Multiregional Sampling. Cancers (Basel) 2023; 15:5826. [PMID: 38136371 PMCID: PMC10741477 DOI: 10.3390/cancers15245826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/09/2023] [Accepted: 12/11/2023] [Indexed: 12/24/2023] Open
Abstract
Glioblastoma (GBM) is an aggressive and highly heterogeneous primary brain tumor. Glioma stem cells represent a subpopulation of tumor cells with stem cell traits that are presumed to be the cause of tumor relapse. There exists complex tumor heterogeneity in drug sensitivity patterns between glioma stem cell (GSC) cultures derived from different patients. Here, we describe that heterogeneity also exists between GSC cultures derived from multiple biopsies within a single tumor. From biopsies harvested within spatially distinct regions representing the entire tumor mass, we established seven GSC cultures and compared their stem cell properties, mutations, gene expression profiles, and drug sensitivity patterns against 115 different anticancer drugs. The results were compared to 14 GSC cultures derived from other patients. Between the multiregional-derived GSC cultures, we observed only minor differences in their phenotype, proliferative capacity, and global gene expression. Further, they displayed intratumoral heterogeneity in mutational profiles and sensitivity patterns to anticancer drugs. This heterogeneity, however, did not exceed the extensive heterogeneity found between GSC cultures derived from other GBM patients. Our results suggest that the use of GSC cultures from one single focal biopsy may underestimate the overall complexity of the GSC population and display the importance of including GSC cultures reflecting the entire tumor mass in drug screening strategies.
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Affiliation(s)
- Marit Brynjulvsen
- Vilhelm Magnus Lab, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Nydalen, P.O. Box 4950, 0424 Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Blindern, P.O. Box 1112, 0317 Oslo, Norway
| | - Elise Solli
- Vilhelm Magnus Lab, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Nydalen, P.O. Box 4950, 0424 Oslo, Norway
| | - Maria Walewska
- Vilhelm Magnus Lab, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Nydalen, P.O. Box 4950, 0424 Oslo, Norway
| | - Manuela Zucknick
- Department of Biostatistics, Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Blindern, P.O. Box 1122, 0317 Oslo, Norway
| | - Luna Djirackor
- Vilhelm Magnus Lab, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Nydalen, P.O. Box 4950, 0424 Oslo, Norway
| | - Iver A. Langmoen
- Vilhelm Magnus Lab, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Nydalen, P.O. Box 4950, 0424 Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Blindern, P.O. Box 1112, 0317 Oslo, Norway
| | - Awais Ahmad Mughal
- Vilhelm Magnus Lab, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Nydalen, P.O. Box 4950, 0424 Oslo, Norway
| | - Erlend Skaga
- Vilhelm Magnus Lab, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Nydalen, P.O. Box 4950, 0424 Oslo, Norway
| | - Einar O. Vik-Mo
- Vilhelm Magnus Lab, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Nydalen, P.O. Box 4950, 0424 Oslo, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Blindern, P.O. Box 1112, 0317 Oslo, Norway
| | - Cecilie J. Sandberg
- Vilhelm Magnus Lab, Institute for Surgical Research and Department of Neurosurgery, Oslo University Hospital, Nydalen, P.O. Box 4950, 0424 Oslo, Norway
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36
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Yabo YA, Moreno-Sanchez PM, Pires-Afonso Y, Kaoma T, Nosirov B, Scafidi A, Ermini L, Lipsa A, Oudin A, Kyriakis D, Grzyb K, Poovathingal SK, Poli A, Muller A, Toth R, Klink B, Berchem G, Berthold C, Hertel F, Mittelbronn M, Heiland DH, Skupin A, Nazarov PV, Niclou SP, Michelucci A, Golebiewska A. Glioblastoma-instructed microglia transition to heterogeneous phenotypic states with phagocytic and dendritic cell-like features in patient tumors and patient-derived orthotopic xenografts. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.05.531162. [PMID: 36945572 PMCID: PMC10028830 DOI: 10.1101/2023.03.05.531162] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
Background A major contributing factor to glioblastoma (GBM) development and progression is its ability to evade the immune system by creating an immune-suppressive environment, where GBM-associated myeloid cells, including resident microglia and peripheral monocyte-derived macrophages, play critical pro-tumoral roles. However, it is unclear whether recruited myeloid cells are phenotypically and functionally identical in GBM patients and whether this heterogeneity is recapitulated in patient-derived orthotopic xenografts (PDOXs). A thorough understanding of the GBM ecosystem and its recapitulation in preclinical models is currently missing, leading to inaccurate results and failures of clinical trials. Methods Here, we report systematic characterization of the tumor microenvironment (TME) in GBM PDOXs and patient tumors at the single-cell and spatial levels. We applied single-cell RNA-sequencing, spatial transcriptomics, multicolor flow cytometry, immunohistochemistry and functional studies to examine the heterogeneous TME instructed by GBM cells. GBM PDOXs representing different tumor phenotypes were compared to glioma mouse GL261 syngeneic model and patient tumors. Results We show that GBM tumor cells reciprocally interact with host cells to create a GBM patient-specific TME in PDOXs. We detected the most prominent transcriptomic adaptations in myeloid cells, with brain-resident microglia representing the main population in the cellular tumor, while peripheral-derived myeloid cells infiltrated the brain at sites of blood-brain barrier disruption. More specifically, we show that GBM-educated microglia undergo transition to diverse phenotypic states across distinct GBM landscapes and tumor niches. GBM-educated microglia subsets display phagocytic and dendritic cell-like gene expression programs. Additionally, we found novel microglial states expressing cell cycle programs, astrocytic or endothelial markers. Lastly, we show that temozolomide treatment leads to transcriptomic plasticity and altered crosstalk between GBM tumor cells and adjacent TME components. Conclusions Our data provide novel insights into the phenotypic adaptation of the heterogeneous TME instructed by GBM tumors. We show the key role of microglial phenotypic states in supporting GBM tumor growth and response to treatment. Our data place PDOXs as relevant models to assess the functionality of the TME and changes in the GBM ecosystem upon treatment.
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Affiliation(s)
- Yahaya A Yabo
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Pilar M Moreno-Sanchez
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Yolanda Pires-Afonso
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Tony Kaoma
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Bakhtiyor Nosirov
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Andrea Scafidi
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Luca Ermini
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
| | - Anuja Lipsa
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
| | - Anaïs Oudin
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
| | - Dimitrios Kyriakis
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Kamil Grzyb
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Suresh K Poovathingal
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
- Single Cell Analytics & Microfluidics Core, Vlaams Instituut voor Biotechnologie-KU Leuven, 3000 Leuven, Belgium
| | - Aurélie Poli
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
| | - Arnaud Muller
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Reka Toth
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Barbara Klink
- National Center of Genetics, Laboratoire National de Santé, L-3555 Dudelange, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
- German Cancer Consortium (DKTK), 01307 Dresden, Germany; Core Unit for Molecular Tumor Diagnostics (CMTD), National Center for Tumor Diseases (NCT), 01307 Dresden, Germany; German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Institute for Clinical Genetics, Faculty of Medicine Carl Gustav Carus, Technische Universität Dresden, 01307 Dresden, Germany
| | - Guy Berchem
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
- Centre Hospitalier Luxembourg, 1210 Luxembourg, Luxembourg
| | | | - Frank Hertel
- Centre Hospitalier Luxembourg, 1210 Luxembourg, Luxembourg
| | - Michel Mittelbronn
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
- Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
- Luxembourg Center of Neuropathology (LCNP), Luxembourg
- National Center of Pathology (NCP), Laboratoire National de Santé, L-3555 Dudelange, Luxembourg
| | - Dieter H Heiland
- Microenvironment and Immunology Research Laboratory, Medical Center - University of Freiburg, Freiburg, Germany
- Department of Neurosurgery, Medical Center - University of Freiburg, Freiburg, Germany
- Department of Neurological Surgery, Lou and Jean Malnati Brain Tumor Institute, Robert H. Lurie Comprehensive Cancer Center, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Alexander Skupin
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
- Department of Physics and Material Science, University Luxembourg, L-4367 Belvaux, Luxembourg
- Department of Neuroscience, University of California San Diego, La Jolla, CA 92093, USA
| | - Petr V Nazarov
- Multiomics Data Science, Department of Cancer Research, Luxembourg Institute of Health, L-1445 Strassen, Luxembourg
| | - Simone P Niclou
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
- Department of Life Sciences and Medicine, Faculty of Science, Technology and Medicine (FSTM), University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Alessandro Michelucci
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
- Neuro-Immunology Group, Department of Cancer Research, Luxembourg Institute of Health, L-1526 Luxembourg, Luxembourg
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Anna Golebiewska
- NORLUX Neuro-Oncology Laboratory, Department of Cancer Research, Luxembourg Institute of Health (LIH), L-1526 Luxembourg, Luxembourg
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Xu H, Zhang Y, Li L, Ren Y, Qian F, Wang L, Ma H, Quan A, Liu H, Yu R. The nanoprodrug of polytemozolomide combines with MGMT siRNA to enhance the effect of temozolomide in glioma. Drug Deliv 2023; 30:1-13. [PMID: 36579448 PMCID: PMC9809344 DOI: 10.1080/10717544.2022.2152911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Temozolomide (TMZ) is a conventional chemotherapeutic drug for glioma, however, its clinical application and efficacy is severely restricted by its drug resistance properties. O6-methylguanine-DNA methyltransferase (MGMT) is a DNA repair enzyme, which can repair the DNA damage caused by TMZ. A large number of clinical data show that reducing the expression of MGMT can enhance the chemotherapeutic efficacy of TMZ. Therefore, in order to improve the resistance of glioma to TMZ, an angiopep-2 (A2) modified nanoprodrug of polytemozolomide (P(TMZ)n) that combines with MGMT siRNA (siMGMT) targeting MGMT was developed (A2/T/D/siMGMT). It not only increased the amount of TMZ within tumor lesion site, but also reduced MGMT expression in glioma. The in vitro experiments indicated that the A2/T/D/siMGMT effectively enhanced the cellular uptake of TMZ and siMGMT, and resulted in a significant cell apoptosis and cytotoxicity in the glioma cells. The in vivo experiments showed that glioma growth was inhibited and the survival time of animals were prolonged remarkably after A2/T/D/siMGMT was injected via tail vein. The results showed that the therapeutic effect of A2/T/D/siMGMT in the treatment of glioma was significantly improved.
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Affiliation(s)
- Haoyue Xu
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China
| | - Yongkang Zhang
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China
| | - Linfeng Li
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China
| | - Yanhong Ren
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China
| | - Feng Qian
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China
| | - Lansheng Wang
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China
| | - Hongwei Ma
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China
| | - Ankang Quan
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China
| | - Hongmei Liu
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China,Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China,Hongmei Liu Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China
| | - Rutong Yu
- Institute of Nervous System Diseases, Xuzhou Medical University, Xuzhou, China,Department of Neurosurgery, Affiliated Hospital of Xuzhou Medical University, Xuzhou, China,CONTACT Yu Rutong;
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Liu Z, Wang S, Yu K, Chen K, Zhao L, Zhang J, Dai K, Zhao P. The promoting effect and mechanism of MAD2L2 on stemness maintenance and malignant progression in glioma. J Transl Med 2023; 21:863. [PMID: 38017538 PMCID: PMC10685699 DOI: 10.1186/s12967-023-04740-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 11/18/2023] [Indexed: 11/30/2023] Open
Abstract
BACKGROUND Glioblastoma, the most common primary malignant tumor of the brain, is associated with poor prognosis. Glioblastoma cells exhibit high proliferative and invasive properties, and glioblastoma stem cells (GSCs) have been shown to play a crucial role in the malignant behavior of glioblastoma cells. This study aims to investigate the molecular mechanisms involved in GSCs maintenance and malignant progression. METHODS Bioinformatics analysis was performed based on data from public databases to explore the expression profile of Mitotic arrest deficient 2 like 2 (MAD2L2) and its potential function in glioma. The impact of MAD2L2 on glioblastoma cell behaviors was assessed through cell viability assays (CCK8), colony formation assays, 5-Ethynyl-2'-deoxyuridine (EDU) incorporation assays, scratch assays, and transwell migration/invasion assays. The findings from in vitro experiments were further validated in vivo using xenograft tumor model. GSCs were isolated from the U87 and LN229 cell lines through flow cytometry and the stemness characteristics were verified by immunofluorescence staining. The sphere-forming ability of GSCs was examined using the stem cell sphere formation assay. Bioinformatics methods were conducted to identified the potential downstream target genes of MAD2L2, followed by in vitro experimental validation. Furthermore, potential upstream transcription factors that regulate MAD2L2 expression were confirmed through chromatin immunoprecipitation (ChIP) and dual-luciferase reporter assays. RESULTS The MAD2L2 exhibited high expression in glioblastoma samples and showed significant correlation with patient prognosis. In vitro and in vivo experiments confirmed that silencing of MAD2L2 led to decreased proliferation, invasion, and migration capabilities of glioblastoma cells, while decreasing stemness characteristics of glioblastoma stem cells. Conversely, overexpression of MAD2L2 enhanced these malignant behaviors. Further investigation revealed that MYC proto-oncogene (c-MYC) mediated the functional role of MAD2L2 in glioblastoma, which was further validated through a rescue experiment. Moreover, using dual-luciferase reporter gene assays and ChIP assays determined that the upstream transcription factor E2F-1 regulated the expression of MAD2L2. CONCLUSION Our study elucidated the role of MAD2L2 in maintaining glioblastoma stemness and promoting malignant behaviors through the regulation of c-MYC, suggesting its potential as a therapeutic target.
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Affiliation(s)
- Zhiyuan Liu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Songtao Wang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
- Putuo People's Hospital, Tongji University, Shanghai, 200060, China
| | - Kuo Yu
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Kaile Chen
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Liang Zhao
- Department of Neurosurgery, The Affiliated Brain Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Jiayue Zhang
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China
| | - Kexiang Dai
- Department of Neurosugery, Emergency General Hospital, Beijing, 100028, China
| | - Peng Zhao
- Department of Neurosurgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210000, China.
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Huang Q, Wang F, Hao D, Li X, Li X, Lei T, Yue J, Liu C. Deciphering tumor-infiltrating dendritic cells in the single-cell era. Exp Hematol Oncol 2023; 12:97. [PMID: 38012715 PMCID: PMC10680280 DOI: 10.1186/s40164-023-00459-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 11/14/2023] [Indexed: 11/29/2023] Open
Abstract
Dendritic cells (DCs) serve as a pivotal link connecting innate and adaptive immunity by processing tumor-derived antigens and activating T cells. The advent of single-cell sequencing has revolutionized the categorization of DCs, enabling a high-resolution characterization of the previously unrecognized diversity of DC populations infiltrating the intricate tumor microenvironment (TME). The application of single-cell sequencing technologies has effectively elucidated the heterogeneity of DCs present in the tumor milieu, yielding invaluable insights into their subpopulation structures and functional diversity. This review provides a comprehensive summary of the current state of knowledge regarding DC subtypes in the TME, drawing from single-cell studies conducted across various human tumors. We focused on the categorization, functions, and interactions of distinct DC subsets, emphasizing their crucial roles in orchestrating tumor-related immune responses. Additionally, we delve into the potential implications of these findings for the identification of predictive biomarkers and therapeutic targets. Enhanced insight into the intricate interplay between DCs and the TME promises to advance our comprehension of tumor immunity and, in turn, pave the way for the development of more efficacious cancer immunotherapies.
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Affiliation(s)
- Qingyu Huang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China
| | - Fuhao Wang
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China
| | - Di Hao
- The Second Clinical Medical College, Anhui Medical University, Hefei, 230032, China
| | - Xinyu Li
- The Second Clinical Medical College, Anhui Medical University, Hefei, 230032, China
| | - Xiaohui Li
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China
| | - Tianyu Lei
- Department of Oncology, Renmin Hospital of Wuhan University, Wuhan, 430060, China
| | - Jinbo Yue
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China.
| | - Chao Liu
- Department of Radiation Oncology, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, 250117, China.
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Heuer S, Winkler F. Glioblastoma revisited: from neuronal-like invasion to pacemaking. Trends Cancer 2023; 9:887-896. [PMID: 37586918 DOI: 10.1016/j.trecan.2023.07.009] [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: 06/01/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 08/18/2023]
Abstract
In recent years, two developments have helped us to better understand the fundamental biology of glioblastoma: the description of a striking intratumoral heterogeneity including gene expression-based cell states, and the discovery that neuro-cancer interactions and cancer-intrinsic neurodevelopmental mechanisms are fundamental features of glioblastoma. In this opinion article, we aim to integrate both developments. We explain how two key disease features are characterized by different neural mechanisms related to distinct but plastic cancer cell states: first, the single cell-dominated invasive parts and second, the more solid parts which are dominated by communicating cell networks constantly activated by pacemaker-like glioblastoma cells. The resulting integrative roadmap of molecular and functional heterogeneity contributes to the Cancer Neuroscience of glioblastoma and suggests novel therapeutic strategies.
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Affiliation(s)
- Sophie Heuer
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 400, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Frank Winkler
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 400, 69120 Heidelberg, Germany; Clinical Cooperation Unit Neurooncology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany.
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Shang E, Sun S, Zhang R, Cao Z, Chen Q, Shi L, Wu J, Wu S, Liu Y, Zheng Y. Overexpression of CD99 is associated with tumor adaptiveness and indicates the tumor recurrence and therapeutic responses in gliomas. Transl Oncol 2023; 37:101759. [PMID: 37579711 PMCID: PMC10440586 DOI: 10.1016/j.tranon.2023.101759] [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: 04/20/2023] [Revised: 07/03/2023] [Accepted: 08/07/2023] [Indexed: 08/16/2023] Open
Abstract
Glioma undergoes adaptive changes, leading to poor prognosis and resistance to treatment. CD99 influences the migration and invasion of glioma cells and plays an oncogene role. However, whether CD99 can affect the adaptiveness of gliomas is still lacking in research, making its clinical value underestimated. Here, we enrolled our in-house and public multiomics datasets for bioinformatic analysis and conducted immunohistochemistry staining to investigate the role of CD99 in glioma adaptive response and its clinical implications. CD99 is expressed in more adaptative glioma subtypes and cell states. Under hypoxic conditions, CD99 is upregulated in glioma cells and is associated with angiogenesis and metabolic adaptations. Gliomas with over-expressed CD99 also increased the immunosuppressive tumor-associated macrophages. The relevance with tumor adaptiveness of CD99 presented clinical significance. We discovered that CD99 overexpression is associated with short-time recurrence and validated its prognostic value. Additionally, Glioma patients with high expression of CD99 were resistant to chemotherapy and radiotherapy. The CD99 expression was also related to anti-angiogenic and immune checkpoint inhibitor therapy response. Inhibitors of the PI3K-AKT pathway have therapeutic potential against CD99-overexpressing gliomas. Our study identified CD99 as a biomarker characterizing the adaptive response in glioma. Gliomas with high CD99 expression are highly tolerant to stress conditions such as hypoxia and antitumor immunity, making treatment responses dimmer and tumor progression. Therefore, for patients with CD99-overexpressing gliomas, tumor adaptiveness should be fully considered during treatment to avoid drug resistance, and closer clinical monitoring should be carried out to improve the prognosis.
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Affiliation(s)
- Erfei Shang
- Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
| | - Shanyue Sun
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China
| | - Ruolan Zhang
- Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
| | - Zehui Cao
- Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
| | - Qingwang Chen
- Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China
| | - Leming Shi
- Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China; Cancer Institute, Shanghai Cancer Center, Fudan University, Shanghai, China
| | - Jinsong Wu
- Glioma Surgery Division, Neurologic Surgery Department of Huashan Hospital, Fudan University, Shanghai, China
| | - Shuai Wu
- Glioma Surgery Division, Neurologic Surgery Department of Huashan Hospital, Fudan University, Shanghai, China.
| | - Yingchao Liu
- Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, China.
| | - Yuanting Zheng
- Human Phenome Institute, School of Life Sciences, Fudan University, Shanghai, China.
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Miller TE, El Farran CA, Couturier CP, Chen Z, D’Antonio JP, Verga J, Villanueva MA, Castro LNG, Tong YE, Saadi TA, Chiocca AN, Fischer DS, Heiland DH, Guerriero JL, Petrecca K, Suva ML, Shalek AK, Bernstein BE. Programs, Origins, and Niches of Immunomodulatory Myeloid Cells in Gliomas. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563466. [PMID: 37961527 PMCID: PMC10634776 DOI: 10.1101/2023.10.24.563466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Gliomas are incurable malignancies notable for an immunosuppressive microenvironment with abundant myeloid cells whose immunomodulatory properties remain poorly defined. Here, utilizing scRNA-seq data for 183,062 myeloid cells from 85 human tumors, we discover that nearly all glioma-associated myeloid cells express at least one of four immunomodulatory activity programs: Scavenger Immunosuppressive, C1Q Immunosuppressive, CXCR4 Inflammatory, and IL1B Inflammatory. All four programs are present in IDH1 mutant and wild-type gliomas and are expressed in macrophages, monocytes, and microglia whether of blood or resident myeloid cell origins. Integrating our scRNA-seq data with mitochondrial DNA-based lineage tracing, spatial transcriptomics, and organoid explant systems that model peripheral monocyte infiltration, we show that these programs are driven by microenvironmental cues and therapies rather than myeloid cell type, origin, or mutation status. The C1Q Immunosuppressive program is driven by routinely administered dexamethasone. The Scavenger Immunosuppressive program includes ligands with established roles in T-cell suppression, is induced in hypoxic regions, and is associated with immunotherapy resistance. Both immunosuppressive programs are less prevalent in lower-grade gliomas, which are instead enriched for the CXCR4 Inflammatory program. Our study provides a framework to understand immunomodulatory myeloid cells in glioma, and a foundation to develop more effective immunotherapies.
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Affiliation(s)
- Tyler E. Miller
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
- Ludwig Center at Harvard Medical School, Boston, MA, USA
| | - Chadi A. El Farran
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
- Ludwig Center at Harvard Medical School, Boston, MA, USA
| | - Charles P. Couturier
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Institute for Medical Engineering and Sciences and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, MA 02115 USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Zeyu Chen
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
| | - Joshua P. D’Antonio
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
| | - Julia Verga
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | - Martin A. Villanueva
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Institute for Medical Engineering and Sciences and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - L. Nicolas Gonzalez Castro
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Center for Neuro-Oncology, Dana-Farber Cancer Institute; Department of Neurology, Brigham and Women’s Hospital, Boston, MA 02115 USA
| | - Yuzhou Evelyn Tong
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Institute for Medical Engineering and Sciences and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Tariq Al Saadi
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Andrew N. Chiocca
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
| | | | - Dieter Henrik Heiland
- Microenvironment and Immunology Research Laboratory, Medical Center - University of Freiburg, Freiburg, Germany. Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, USA
| | - Jennifer L. Guerriero
- Ludwig Center at Harvard Medical School, Boston, MA, USA
- Breast Oncology Program, Dana-Farber Cancer Institute; Division of Breast Surgery, Department of Surgery, Brigham and Women’s Hospital, Boston, MA, USA
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Mario L. Suva
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Alex K. Shalek
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Institute for Medical Engineering and Sciences and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Bradley E. Bernstein
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Department of Cancer Biology, Dana Farber Cancer Institute, Boston, MA 02215, USA
- Department of Cell Biology and Pathology, Harvard Medical School, Boston, MA 02215, USA
- Ludwig Center at Harvard Medical School, Boston, MA, USA
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Green MV, Gallegos DA, Boua JV, Bartelt LC, Narayanan A, West AE. Single-Nucleus Transcriptional Profiling of GAD2-Positive Neurons From Mouse Lateral Habenula Reveals Distinct Expression of Neurotransmission- and Depression-Related Genes. BIOLOGICAL PSYCHIATRY GLOBAL OPEN SCIENCE 2023; 3:686-697. [PMID: 37881543 PMCID: PMC10593960 DOI: 10.1016/j.bpsgos.2023.04.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 04/17/2023] [Accepted: 04/18/2023] [Indexed: 10/27/2023] Open
Abstract
Background Glutamatergic projection neurons of the lateral habenula (LHb) drive behavioral state modulation by regulating the activity of midbrain monoaminergic neurons. Identifying circuit mechanisms that modulate LHb output is of interest for understanding control of motivated behaviors. Methods A small population of neurons within the medial subnucleus of the mouse LHb express the GABAergic (gamma-aminobutyric acidergic)-synthesizing enzyme GAD2, and they can inhibit nearby LHb projection neurons; however, these neurons lack markers of classic inhibitory interneurons, and they coexpress the vesicular glutamate transporter VGLUT2. To determine the molecular phenotype of these neurons, we genetically tagged the nuclei of GAD2-positive cells and used fluorescence-activated nuclear sorting to isolate and enrich these nuclei for single-nucleus RNA sequencing. Results Our data confirm that GAD2+/VGLUT2+ neurons intrinsic to the LHb coexpress markers of both glutamatergic and GABAergic transmission and that they are transcriptionally distinct from either GABAergic interneurons or habenular glutamatergic neurons. We identify gene expression programs within these cells that show sex-specific differences in expression and that are implicated in major depressive disorder, which has been linked to LHb hyperactivity. Finally, we identify the Ntng2 gene encoding the cell adhesion protein netrin-G2 as a marker of LHb GAD2+/VGLUT2+ neurons and a gene product that may contribute to their target projections. Conclusions These data show the value of using genetic enrichment of rare cell types for transcriptome studies, and they advance understanding of the molecular composition of a functionally important class of GAD2+ neurons in the LHb.
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Affiliation(s)
- Matthew V. Green
- Department of Neurobiology, Duke University, Durham, North Carolina
| | | | | | - Luke C. Bartelt
- Department of Neurobiology, Duke University, Durham, North Carolina
| | - Arthy Narayanan
- Department of Neurobiology, Duke University, Durham, North Carolina
| | - Anne E. West
- Department of Neurobiology, Duke University, Durham, North Carolina
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Riviere-Cazaux C, Neth BJ, Hoplin MD, Wessel B, Miska J, Kizilbash SH, Burns TC. Glioma Metabolic Feedback In Situ: A First-In-Human Pharmacodynamic Trial of Difluoromethylornithine + AMXT-1501 Through High-Molecular Weight Microdialysis. Neurosurgery 2023; 93:932-938. [PMID: 37246885 PMCID: PMC10637404 DOI: 10.1227/neu.0000000000002511] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 03/07/2023] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND AND OBJECTIVES No new drug has improved survival for glioblastoma since temozolomide in 2005, due in part to the relative inaccessibility of each patient's individualized tumor biology and its response to therapy. We have identified a conserved extracellular metabolic signature of enhancing high-grade gliomas enriched for guanidinoacetate (GAA). GAA is coproduced with ornithine, the precursor to protumorigenic polyamines through ornithine decarboxylase (ODC). AMXT-1501 is a polyamine transporter inhibitor that can overcome tumoral resistance to the ODC inhibitor, difluoromethylornithine (DFMO). We will use DFMO with or without AMXT-1501 to identify candidate pharmacodynamic biomarkers of polyamine depletion in patients with high-grade gliomas in situ . We aim to determine (1) how blocking polyamine production affects intratumoral extracellular guanidinoacetate abundance and (2) the impact of polyamine depletion on the global extracellular metabolome within live human gliomas in situ. METHODS DFMO, with or without AMXT-1501, will be administered postoperatively in 15 patients after clinically indicated subtotal resection for high-grade glioma. High-molecular weight microdialysis catheters implanted into residual tumor and adjacent brain will be used for postoperative monitoring of extracellular GAA and polyamines throughout therapeutic intervention from postoperative day (POD) 1 to POD5. Catheters will be removed on POD5 before discharge. EXPECTED OUTCOMES We anticipate that GAA will be elevated in tumor relative to adjacent brain although it will decrease within 24 hours of ODC inhibition with DFMO. If AMXT-1501 effectively increases the cytotoxic impact of ODC inhibition, we expect an increase in biomarkers of cytotoxicity including glutamate with DFMO + AMXT-1501 treatment when compared with DFMO alone. DISCUSSION Limited mechanistic feedback from individual patients' gliomas hampers clinical translation of novel therapies. This pilot Phase 0 study will provide in situ feedback during DFMO + AMXT-1501 treatment to determine how high-grade gliomas respond to polyamine depletion.
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Affiliation(s)
| | - Bryan J. Neth
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | - Matthew D. Hoplin
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Bambi Wessel
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Jason Miska
- Department of Neurological Surgery, Northwestern University, Chicago, Illinois, USA
| | | | - Terry C. Burns
- Department of Neurological Surgery, Mayo Clinic, Rochester, Minnesota, USA
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Drexler R, Sauvigny T, Schüller U, Eckhardt A, Maire CL, Khatri R, Hausmann F, Hänzelmann S, Huber TB, Bonn S, Bode H, Lamszus K, Westphal M, Dührsen L, Ricklefs FL. Epigenetic profiling reveals a strong association between lack of 5-ALA fluorescence and EGFR amplification in IDH-wildtype glioblastoma. Neurooncol Pract 2023; 10:462-471. [PMID: 37720395 PMCID: PMC10502788 DOI: 10.1093/nop/npad025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/19/2023] Open
Abstract
Background 5-aminolevulinic acid (5-ALA) fluorescence-guided resection increases the percentage of complete CNS tumor resections and improves the progression-free survival of IDH-wildtype glioblastoma patients. A small subset of IDH-wildtype glioblastoma shows no 5-ALA fluorescence. An explanation for these cases is missing. In this study, we used DNA methylation profiling to further characterize non-fluorescent glioblastomas. Methods Patients with newly diagnosed and recurrent IDH-wildtype glioblastoma that underwent surgery were analyzed. The intensity of intraoperative 5-ALA fluorescence was categorized as non-visible or visible. DNA was extracted from tumors and genome-wide DNA methylation patterns were analyzed using Illumina EPIC (850k) arrays. Furthermore, 5-ALA intensity was measured by flow cytometry on human gliomasphere lines (BT112 and BT145). Results Of 74 included patients, 12 (16.2%) patients had a non-fluorescent glioblastoma, which were compared to 62 glioblastomas with 5-ALA fluorescence. Clinical characteristics were equally distributed between both groups. We did not find significant differences between DNA methylation subclasses and 5-ALA fluorescence (P = .24). The distribution of cells of the tumor microenvironment was not significantly different between the non-fluorescent and fluorescent tumors. Copy number variations in EGFR and simultaneous EGFRvIII expression were strongly associated with 5-ALA fluorescence since all non-fluorescent glioblastomas were EGFR-amplified (P < .01). This finding was also demonstrated in recurrent tumors. Similarly, EGFR-amplified glioblastoma cell lines showed no 5-ALA fluorescence after 24 h of incubation. Conclusions Our study demonstrates an association between non-fluorescent IDH-wildtype glioblastomas and EGFR gene amplification which should be taken into consideration for recurrent surgery and future studies investigating EGFR-amplified gliomas.
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Affiliation(s)
- Richard Drexler
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Sauvigny
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, Research Institute Children’s Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
| | - Alicia Eckhardt
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Lab of Radiobiology & Experimental Radiation Oncology, University Cancer Center Hamburg, Hamburg, Germany
- Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
| | - Cecile L Maire
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Robin Khatri
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fabian Hausmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sonja Hänzelmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Huber
- Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Helena Bode
- Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lasse Dührsen
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Franz L Ricklefs
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Ashouri A, Zhang C, Gaiti F. Decoding Cancer Evolution: Integrating Genetic and Non-Genetic Insights. Genes (Basel) 2023; 14:1856. [PMID: 37895205 PMCID: PMC10606072 DOI: 10.3390/genes14101856] [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: 09/01/2023] [Revised: 09/19/2023] [Accepted: 09/22/2023] [Indexed: 10/29/2023] Open
Abstract
The development of cancer begins with cells transitioning from their multicellular nature to a state akin to unicellular organisms. This shift leads to a breakdown in the crucial regulators inherent to multicellularity, resulting in the emergence of diverse cancer cell subpopulations that have enhanced adaptability. The presence of different cell subpopulations within a tumour, known as intratumoural heterogeneity (ITH), poses challenges for cancer treatment. In this review, we delve into the dynamics of the shift from multicellularity to unicellularity during cancer onset and progression. We highlight the role of genetic and non-genetic factors, as well as tumour microenvironment, in promoting ITH and cancer evolution. Additionally, we shed light on the latest advancements in omics technologies that allow for in-depth analysis of tumours at the single-cell level and their spatial organization within the tissue. Obtaining such detailed information is crucial for deepening our understanding of the diverse evolutionary paths of cancer, allowing for the development of effective therapies targeting the key drivers of cancer evolution.
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Affiliation(s)
- Arghavan Ashouri
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
| | - Chufan Zhang
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Federico Gaiti
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON M5G 2M9, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
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Zhang S, Guo Y, Hu Y, Gao X, Bai F, Ding Q, Hou K, Wang Z, Sun X, Zhao H, Qu Z, Xu Q. The role of APOBEC3C in modulating the tumor microenvironment and stemness properties of glioma: evidence from pancancer analysis. Front Immunol 2023; 14:1242972. [PMID: 37809064 PMCID: PMC10551170 DOI: 10.3389/fimmu.2023.1242972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Background It is now understood that APOBEC3 family proteins (A3s) are essential in tumor progression, yet their involvement in tumor immunity and stemness across diverse cancer types remains poorly understood. Methods In the present study, comprehensive genome-wide statistical and bioinformatic analyses were conducted to elucidate A3 family expression patterns, establishing clinically relevant correlations with prognosis, the tumor microenvironment(TME), immune infiltration, checkpoint blockade, and stemness across cancers. Different experimental techniques were applied, including RT-qPCR, immunohistochemistry, sphere formation assays, Transwell migration assays, and wound-healing assays, to investigate the impact of A3C on low-grade glioma (LGG) and glioblastoma multiforme (GBM), as well as its function in glioma stem cells(GSCs). Results Dysregulated expression of A3s was observed in various human cancer tissues. The prognostic value of A3 expression differed across cancer types, with a link to particularly unfavorable outcomes in gliomas. A3s are associated with the the TME and stemness in multiple cancers. Additionally, we developed an independent prognostic model based on A3s expression, which may be an independent prognostic factor for OS in patients with glioma. Subsequent validation underscored a strong association between elevated A3C expression and adverse prognostic outcomes, higher tumor grades, and unfavorable histology in glioma. A potential connection between A3C and glioma progression was established. Notably, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses implicated A3C in immune system-related diseases, with heightened A3C levels contributing to an immunosuppressive tumor microenvironment (TME) in glioma. Furthermore, in vitro experiments substantiated the role of A3C in sustaining and renewing glioma stem cells, as A3C deletion led to diminished proliferation, invasion, and migration of glioma cells. Conclusion The A3 family exhibits heterogeneous expression across various cancer types, with its expression profile serving as a predictive marker for overall survival in glioma patients. A3C emerges as a regulator of glioma progression, exerting its influence through modulation of the tumor microenvironment and regulation of stemness.
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Affiliation(s)
- Shoudu Zhang
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Yugang Guo
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Yuanzheng Hu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Xiaofang Gao
- The Department of Science and Technology, Zhengzhou Revogene Ltd, Zhengzhou, Henan, China
| | - Fanghui Bai
- Department of Oncology, Nanyang central Hospital, Nanyang, Henan, China
| | - Qian Ding
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Kaiqi Hou
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Zongqing Wang
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
| | - Xing Sun
- Department of Oncology, Nanyang central Hospital, Nanyang, Henan, China
| | - Hui Zhao
- The Department of Science and Technology, Zhengzhou Revogene Ltd, Zhengzhou, Henan, China
| | - Zhongyu Qu
- Department of Oncology, Nanyang central Hospital, Nanyang, Henan, China
| | - Qian Xu
- Henan Provincial Engineering Laboratory of Insects Bio-reactor, Nanyang Normal University, Nanyang, Henan, China
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Wu Y, Mao M, Wang LJ. Integrated clustering signature of genomic heterogeneity, stemness and tumor microenvironment predicts glioma prognosis and immunotherapy response. Aging (Albany NY) 2023; 15:9086-9104. [PMID: 37698534 PMCID: PMC10522363 DOI: 10.18632/aging.205018] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/21/2023] [Indexed: 09/13/2023]
Abstract
BACKGROUND Glioma is the most frequent primary tumor of the central nervous system. The high heterogeneity of glioma tumors enables them to adapt to challenging environments, leading to resistance to treatment. Therefore, to detect the driving factors and improve the prognosis of glioma, it is essential to have a comprehensive understanding of the genomic heterogeneity, stemness, and immune microenvironment of glioma. METHODS We classified gliomas into various subtypes based on stemness, genomic heterogeneity, and immune microenvironment consensus clustering analysis. We identified risk hub genes linked to heterogeneous characteristics using WGCNA, LASSO, and multivariate Cox regression analysis and utilized them to create an effective risk model. RESULTS We thoroughly investigated the genomic heterogeneity, stemness, and immune microenvironment of glioma and identified the risk hub genes RAB42, SH2D4A, and GDF15 based on the TCGA dataset. We developed a risk model utilizing these genes that can reliably predict the prognosis of glioma patients. The risk signature showed a positive correlation with T cell exhaustion and increased infiltration of immunosuppressive cells, and a negative correlation with the response to immunotherapy. Moreover, we discovered that SH2D4A, one of the risk hub genes, could stimulate the migration and proliferation of glioma cells. CONCLUSIONS This study identified risk hub genes and established a risk model by analyzing the genomic heterogeneity, stemness, and immune microenvironment of glioma. Our findings will facilitate the diagnosis and prediction of glioma prognosis and may lead to potential treatment strategies for glioma.
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Affiliation(s)
- Yangyang Wu
- Advanced Medical Research Center of Zhengzhou University, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, China
| | - Meng Mao
- Advanced Medical Research Center of Zhengzhou University, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, China
- Department of Anesthesiology and Perioperative Medicine, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, China
- Research of Trauma Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, China
| | - Lin-Jian Wang
- Advanced Medical Research Center of Zhengzhou University, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, China
- Research of Trauma Center, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, China
- Department of Neurosurgery, Zhengzhou Central Hospital Affiliated to Zhengzhou University, Zhengzhou 450007, China
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Jane EP, Reslink MC, Gatesman TA, Halbert ME, Miller TA, Golbourn BJ, Casillo SM, Mullett SJ, Wendell SG, Obodo U, Mohanakrishnan D, Dange R, Michealraj A, Brenner C, Agnihotri S, Premkumar DR, Pollack IF. Targeting mitochondrial energetics reverses panobinostat- and marizomib-induced resistance in pediatric and adult high-grade gliomas. Mol Oncol 2023; 17:1821-1843. [PMID: 37014128 PMCID: PMC10483615 DOI: 10.1002/1878-0261.13427] [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: 11/08/2022] [Revised: 02/22/2023] [Accepted: 04/03/2023] [Indexed: 04/05/2023] Open
Abstract
In previous studies, we demonstrated that panobinostat, a histone deacetylase inhibitor, and bortezomib, a proteasomal inhibitor, displayed synergistic therapeutic activity against pediatric and adult high-grade gliomas. Despite the remarkable initial response to this combination, resistance emerged. Here, in this study, we aimed to investigate the molecular mechanisms underlying the anticancer effects of panobinostat and marizomib, a brain-penetrant proteasomal inhibitor, and the potential for exploitable vulnerabilities associated with acquired resistance. RNA sequencing followed by gene set enrichment analysis (GSEA) was employed to compare the molecular signatures enriched in resistant compared with drug-naïve cells. The levels of adenosine 5'-triphosphate (ATP), nicotinamide adenine dinucleotide (NAD)+ content, hexokinase activity, and tricarboxylic acid (TCA) cycle metabolites required for oxidative phosphorylation to meet their bioenergetic needs were analyzed. Here, we report that panobinostat and marizomib significantly depleted ATP and NAD+ content, increased mitochondrial permeability and reactive oxygen species generation, and promoted apoptosis in pediatric and adult glioma cell lines at initial treatment. However, resistant cells exhibited increased levels of TCA cycle metabolites, which required for oxidative phosphorylation to meet their bioenergetic needs. Therefore, we targeted glycolysis and the electron transport chain (ETC) with small molecule inhibitors, which displayed substantial efficacy, suggesting that resistant cell survival is dependent on glycolytic and ETC complexes. To verify these observations in vivo, lonidamine, an inhibitor of glycolysis and mitochondrial function, was chosen. We produced two diffuse intrinsic pontine glioma (DIPG) models, and lonidamine treatment significantly increased median survival in both models, with particularly dramatic effects in panobinostat- and marizomib-resistant cells. These data provide new insights into mechanisms of treatment resistance in gliomas.
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Affiliation(s)
- Esther P. Jane
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
- John G. Rangos Sr. Research CenterChildren's Hospital of PittsburghPAUSA
| | - Matthew C. Reslink
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
| | - Taylor A. Gatesman
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
- John G. Rangos Sr. Research CenterChildren's Hospital of PittsburghPAUSA
| | - Matthew E. Halbert
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
- John G. Rangos Sr. Research CenterChildren's Hospital of PittsburghPAUSA
| | - Tracy A. Miller
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
| | - Brian J. Golbourn
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
| | - Stephanie M. Casillo
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
- John G. Rangos Sr. Research CenterChildren's Hospital of PittsburghPAUSA
| | - Steven J. Mullett
- Department of Pharmacology and Chemical BiologyUniversity of PittsburghPAUSA
| | - Stacy G. Wendell
- Department of Pharmacology and Chemical BiologyUniversity of PittsburghPAUSA
| | - Udochukwu Obodo
- Department of Diabetes & Cancer MetabolismCity of Hope Medical CenterDuarteCAUSA
| | | | - Riya Dange
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
| | - Antony Michealraj
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
| | - Charles Brenner
- Department of Diabetes & Cancer MetabolismCity of Hope Medical CenterDuarteCAUSA
| | - Sameer Agnihotri
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
- John G. Rangos Sr. Research CenterChildren's Hospital of PittsburghPAUSA
- UPMC Hillman Cancer CenterPittsburghPAUSA
| | - Daniel R. Premkumar
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
- John G. Rangos Sr. Research CenterChildren's Hospital of PittsburghPAUSA
- UPMC Hillman Cancer CenterPittsburghPAUSA
| | - Ian F. Pollack
- Department of NeurosurgeryUniversity of Pittsburgh School of MedicinePAUSA
- John G. Rangos Sr. Research CenterChildren's Hospital of PittsburghPAUSA
- UPMC Hillman Cancer CenterPittsburghPAUSA
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50
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Sattiraju A, Kang S, Giotti B, Chen Z, Marallano VJ, Brusco C, Ramakrishnan A, Shen L, Tsankov AM, Hambardzumyan D, Friedel RH, Zou H. Hypoxic niches attract and sequester tumor-associated macrophages and cytotoxic T cells and reprogram them for immunosuppression. Immunity 2023; 56:1825-1843.e6. [PMID: 37451265 PMCID: PMC10527169 DOI: 10.1016/j.immuni.2023.06.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 02/24/2023] [Accepted: 06/19/2023] [Indexed: 07/18/2023]
Abstract
Glioblastoma (GBM), a highly lethal brain cancer, is notorious for immunosuppression, but the mechanisms remain unclear. Here, we documented a temporospatial patterning of tumor-associated myeloid cells (TAMs) corresponding to vascular changes during GBM progression. As tumor vessels transitioned from the initial dense regular network to later scant and engorged vasculature, TAMs shifted away from perivascular regions and trafficked to vascular-poor areas. This process was heavily influenced by the immunocompetence state of the host. Utilizing a sensitive fluorescent UnaG reporter to track tumor hypoxia, coupled with single-cell transcriptomics, we revealed that hypoxic niches attracted and sequestered TAMs and cytotoxic T lymphocytes (CTLs), where they were reprogrammed toward an immunosuppressive state. Mechanistically, we identified chemokine CCL8 and cytokine IL-1β as two hypoxic-niche factors critical for TAM trafficking and co-evolution of hypoxic zones into pseudopalisading patterns. Therefore, perturbation of TAM patterning in hypoxic zones may improve tumor control.
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Affiliation(s)
- Anirudh Sattiraju
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Sangjo Kang
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Bruno Giotti
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Zhihong Chen
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Valerie J Marallano
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Concetta Brusco
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Aarthi Ramakrishnan
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Li Shen
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander M Tsankov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dolores Hambardzumyan
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Oncological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Roland H Friedel
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Hongyan Zou
- Nash Family Department of Neuroscience, Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
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