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Jilani M, Degras D, Haspel N. Elucidating Cancer Subtypes by Using the Relationship between DNA Methylation and Gene Expression. Genes (Basel) 2024; 15:631. [PMID: 38790260 PMCID: PMC11121157 DOI: 10.3390/genes15050631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/10/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Advancements in the field of next generation sequencing (NGS) have generated vast amounts of data for the same set of subjects. The challenge that arises is how to combine and reconcile results from different omics studies, such as epigenome and transcriptome, to improve the classification of disease subtypes. In this study, we introduce sCClust (sparse canonical correlation analysis with clustering), a technique to combine high-dimensional omics data using sparse canonical correlation analysis (sCCA), such that the correlation between datasets is maximized. This stage is followed by clustering the integrated data in a lower-dimensional space. We apply sCClust to gene expression and DNA methylation data for three cancer genomics datasets from the Cancer Genome Atlas (TCGA) to distinguish between underlying subtypes. We evaluate the identified subtypes using Kaplan-Meier plots and hazard ratio analysis on the three types of cancer-GBM (glioblastoma multiform), lung cancer and colon cancer. Comparison with subtypes identified by both single- and multi-omics studies implies improved clinical association. We also perform pathway over-representation analysis in order to identify up-regulated and down-regulated genes as tentative drug targets. The main goal of the paper is twofold: the integration of epigenomic and transcriptomic datasets followed by elucidating subtypes in the latent space. The significance of this study lies in the enhanced categorization of cancer data, which is crucial to precision medicine.
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Affiliation(s)
- Muneeba Jilani
- Department of Computer Science, University of Massachusetts Boston, Boston, MA 02125, USA;
| | - David Degras
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Nurit Haspel
- Department of Computer Science, University of Massachusetts Boston, Boston, MA 02125, USA;
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2
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Chen S, Wang H, Guo M, Zhao X, Yang J, Chen L, Zhao J, Chen C, Zhou Y, Xu L. Promoter A1312C mutation leads to microRNA-7 downregulation in human non-small cell lung cancer. Cell Signal 2024; 117:111095. [PMID: 38346527 DOI: 10.1016/j.cellsig.2024.111095] [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: 01/02/2024] [Revised: 01/26/2024] [Accepted: 02/09/2024] [Indexed: 02/16/2024]
Abstract
MicroRNA-7 (miRNA-7, miR-7) is a unique class of tumor suppressors, plays an important role in various physiological and pathological processes including human non-small cell lung cancer (NSCLC). In previous works, we revealed that miR-7 could regulate the growth and metastasis of human NSCLC cells. However, the mechanism of dysregulated miR-7 expression in NSCLC remains to be further elucidated. In this study, based on clinical sample analysis, we found that the downregulated expression of miR-7 was dominantly attributed to the decreased level of pri-miR-7-2 in human NSCLC. Furthermore, there were four site mutations in the miR-7-2 promoter sequence. Notably, among these four sites, mutation at -1312 locus (A → C, termed as A1312C mutation) was dominate, and A1312C mutation further led to decreased expression of miR-7 in human NSCLC cells, accompanied with elevated transduction of NDUFA4/ERK/AKT signaling pathway. Mechanistically, homeobox A5 (HOXA5) is the key transcription factors regulating miR-7 expression in NSCLC. A1312C mutation impairs HOXA5 binding, thereby reducing the transcriptional activity of miR-7-2 promoter, resulting in downregulation of miR-7 expression. Together, these data may provide new insights into the dysregulation of specific miRNA expression in NSCLC and ultimately prove to be helpful in the diagnostic, prognostic, and therapeutic strategies against NSCLC.
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Affiliation(s)
- Shipeng Chen
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi 563000, China; Department of Immunology, Zunyi Medical University, Zunyi 563000, Guizhou, China
| | - Hui Wang
- The Second Affiliated Hospital of Zunyi Medical University, Zunyi 563000, Guizhou, China
| | - Mengmeng Guo
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi 563000, China; Department of Immunology, Zunyi Medical University, Zunyi 563000, Guizhou, China
| | - Xu Zhao
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi 563000, China; Department of Immunology, Zunyi Medical University, Zunyi 563000, Guizhou, China
| | - Jing Yang
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi 563000, China; Department of Immunology, Zunyi Medical University, Zunyi 563000, Guizhou, China
| | - Longqing Chen
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi 563000, China; Department of Immunology, Zunyi Medical University, Zunyi 563000, Guizhou, China
| | - Juanjuan Zhao
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi 563000, China; Department of Immunology, Zunyi Medical University, Zunyi 563000, Guizhou, China
| | - Chao Chen
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi 563000, China; Department of Immunology, Zunyi Medical University, Zunyi 563000, Guizhou, China.
| | - Ya Zhou
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi 563000, China; Department of Medical Physics, Zunyi Medical University, Zunyi 563000, Guizhou, China.
| | - Lin Xu
- Special Key Laboratory of Gene Detection and Therapy of Guizhou Province, Zunyi 563000, China; Department of Immunology, Zunyi Medical University, Zunyi 563000, Guizhou, China; Collaborative Innovation Center of Tissue Damage Repair and Regeneration Medicine of Zunyi Medical University, Zunyi, Guizhou 563000, China.
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3
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Nuechterlein N, Shelbourn A, Szulzewsky F, Arora S, Casad M, Pattwell S, Merino-Galan L, Sulman E, Arowa S, Alvinez N, Jung M, Brown D, Tang K, Jackson S, Stoica S, Chittaboina P, Banasavadi-Siddegowda YK, Wirsching HG, Stella N, Shapiro L, Paddison P, Patel AP, Gilbert MR, Abdullaev Z, Aldape K, Pratt D, Holland EC, Cimino PJ. Haploinsufficiency of phosphodiesterase 10A activates PI3K/AKT signaling independent of PTEN to induce an aggressive glioma phenotype. Genes Dev 2024; 38:273-288. [PMID: 38589034 PMCID: PMC11065166 DOI: 10.1101/gad.351350.123] [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: 03/27/2024] [Indexed: 04/10/2024]
Abstract
Glioblastoma is universally fatal and characterized by frequent chromosomal copy number alterations harboring oncogenes and tumor suppressors. In this study, we analyzed exome-wide human glioblastoma copy number data and found that cytoband 6q27 is an independent poor prognostic marker in multiple data sets. We then combined CRISPR-Cas9 data, human spatial transcriptomic data, and human and mouse RNA sequencing data to nominate PDE10A as a potential haploinsufficient tumor suppressor in the 6q27 region. Mouse glioblastoma modeling using the RCAS/tv-a system confirmed that Pde10a suppression induced an aggressive glioma phenotype in vivo and resistance to temozolomide and radiation therapy in vitro. Cell culture analysis showed that decreased Pde10a expression led to increased PI3K/AKT signaling in a Pten-independent manner, a response blocked by selective PI3K inhibitors. Single-nucleus RNA sequencing from our mouse gliomas in vivo, in combination with cell culture validation, further showed that Pde10a suppression was associated with a proneural-to-mesenchymal transition that exhibited increased cell adhesion and decreased cell migration. Our results indicate that glioblastoma patients harboring PDE10A loss have worse outcomes and potentially increased sensitivity to PI3K inhibition.
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Affiliation(s)
- Nicholas Nuechterlein
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Allison Shelbourn
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Frank Szulzewsky
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Sonali Arora
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Michelle Casad
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington 98195, USA
| | - Siobhan Pattwell
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington 98145, USA
| | - Leyre Merino-Galan
- Ben Towne Center for Childhood Cancer Research, Seattle Children's Research Institute, Seattle, Washington 98145, USA
| | - Erik Sulman
- Department of Radiation Oncology, New York University Grossman School of Medicine, New York, New York 11220, USA
| | - Sumaita Arowa
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Neriah Alvinez
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Miyeon Jung
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Desmond Brown
- Neurosurgical Oncology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Kayen Tang
- Developmental Therapeutics and Pharmacology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Sadhana Jackson
- Developmental Therapeutics and Pharmacology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Stefan Stoica
- Neurosurgery Unit for Pituitary and Inheritable Diseases, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Prashant Chittaboina
- Neurosurgery Unit for Pituitary and Inheritable Diseases, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Yeshavanth K Banasavadi-Siddegowda
- Molecular and Therapeutics Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Hans-Georg Wirsching
- Department of Neurology, University Hospital, University of Zurich, Zurich 8091, Switzerland
| | - Nephi Stella
- Department of Pharmacology, University of Washington, Seattle, Washington 98195, USA
| | - Linda Shapiro
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA
| | - Patrick Paddison
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Anoop P Patel
- Department of Neurosurgery, Preston Robert Tisch Brain Tumor Center, Duke University, Durham, North Carolina 27710, USA
| | - Mark R Gilbert
- Neuro-Oncology Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Kenneth Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Drew Pratt
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20814, USA
| | - Eric C Holland
- Human Biology Division, Fred Hutchinson Cancer Center, Seattle, Washington 98109, USA
| | - Patrick J Cimino
- Neuropathology Unit, Surgical Neurology Branch, National Institute of Neurological Disorders and Stroke, National Institutes of Health, Bethesda, Maryland 20814, USA;
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4
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Mamatjan Y, Voisin MR, Nassiri F, Moraes FY, Bunda S, So J, Salih M, Shirahata M, Ono T, Shimizu H, Schrimpf D, von Deimling A, Aldape KD, Zadeh G. Integrated molecular analysis reveals hypermethylation and overexpression of HOX genes to be poor prognosticators in isocitrate dehydrogenase mutant glioma. Neuro Oncol 2023; 25:2028-2041. [PMID: 37474126 PMCID: PMC10628942 DOI: 10.1093/neuonc/noad126] [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: 02/02/2023] [Indexed: 07/22/2023] Open
Abstract
BACKGROUND Diffuse gliomas represent over 80% of malignant brain tumors ranging from low-grade to aggressive high-grade lesions. Within isocitrate dehydrogenase (IDH)-mutant gliomas, there is a high variability in survival and a need to more accurately predict outcome. METHODS To identify and characterize a predictive signature of outcome in gliomas, we utilized an integrative molecular analysis (using methylation, mRNA, copy number variation (CNV), and mutation data), analyzing a total of 729 IDH-mutant samples including a test set of 99 from University Health Network (UHN) and 2 validation cohorts including the German Cancer Research Center (DKFZ) and The Cancer Genome Atlas (TCGA). RESULTS Cox regression analysis of methylation data from the UHN cohort identified CpG-based signatures that split the glioma cohort into 2 prognostic groups strongly predicting survival that were validated using 2 independent cohorts from TCGA and DKFZ (all P-values < .0001). The methylation signatures that predicted poor outcomes also exhibited high CNV instability and hypermethylation of HOX gene probes. Integrated multi-platform analyses using mRNA and methylation (iRM) showed that parallel HOX gene overexpression and simultaneous hypermethylation were significantly associated with increased mutational load, high aneuploidy, and worse survival (P-value < .0001). A 7-HOX gene signature was developed and validated using the most significantly associated HOX genes with patient outcome in both 1p/19q codeleted and non-codeleted IDHmut gliomas. CONCLUSIONS HOX gene methylation and expression provide important prognostic information in IDH-mutant gliomas that are not captured by current molecular diagnostics. A 7-HOX gene signature of outcome shows significant survival differences in both 1p/19q codeleted and non-codeleted IDH-mutant gliomas.
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Affiliation(s)
- Yasin Mamatjan
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
- Faculty of Science, Thompson Rivers University, Kamloops, British Columbia, Canada
| | - Mathew R Voisin
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
| | - Farshad Nassiri
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
| | - Fabio Y Moraes
- Department of Oncology, Queens University, Kingston, Ontario, Canada
| | - Severa Bunda
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
| | - Jonathan So
- Department of Medicine, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Mira Salih
- Mount Sinai Hospital, New York, New York, USA
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Mitsuaki Shirahata
- Department of Neuro-Oncology/Neurosurgery, Saitama Medical University International Medical Center, Hidaka, Japan
| | - Takahiro Ono
- Department of Neurosurgery, Akita University Graduate School of Medicine, Akita, Japan
| | - Hiroaki Shimizu
- Department of Neurosurgery, Akita University Graduate School of Medicine, Akita, Japan
| | - Daniel Schrimpf
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, Heidelberg University Hospital, Heidelberg, Germany
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, USA
| | - Gelareh Zadeh
- Princess Margaret Cancer Center and MacFeeters-Hamilton Center for Neuro-Oncology Research, University Health Network, Toronto, Ontario, Canada
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5
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Göbel C, Godbole S, Schoof M, Holdhof D, Kresbach C, Loose C, Neumann J, Schüller U. MYC overexpression and SMARCA4 loss cooperate to drive medulloblastoma formation in mice. Acta Neuropathol Commun 2023; 11:174. [PMID: 37919824 PMCID: PMC10621315 DOI: 10.1186/s40478-023-01654-2] [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: 07/12/2023] [Accepted: 09/17/2023] [Indexed: 11/04/2023] Open
Abstract
Group 3 medulloblastoma is one of the most aggressive types of childhood brain tumors. Roughly 30% of cases carry genetic alterations in MYC, SMARCA4, or both genes combined. While overexpression of MYC has previously been shown to drive medulloblastoma formation in mice, the functional significance of SMARCA4 mutations and their suitability as a therapeutic target remain largely unclear. To address this issue, we combined overexpression of MYC with a loss of SMARCA4 in granule cell precursors. Both alterations did not increase proliferation of granule cell precursors in vitro. However, combined MYC overexpression and SMARCA4 loss successfully induced tumor formation in vivo after orthotopic transplantation in recipient mice. Resulting tumors displayed anaplastic histology and exclusively consisted of SMARCA4-negative cells although a mixture of recombined and non-recombined cells was injected. These observations provide first evidence for a tumor-promoting role of a SMARCA4 deficiency in the development of medulloblastoma. In comparing the transcriptome of tumors to the cells of origin and an established Sonic Hedgehog medulloblastoma model, we gathered first hints on deregulated gene expression that could be specifically involved in SMARCA4/MYC driven tumorigenesis. Finally, an integration of RNA sequencing and DNA methylation data of murine tumors with human samples revealed a high resemblance to human Group 3 medulloblastoma on the molecular level. Altogether, the development of SMARCA4-deficient medulloblastomas in mice paves the way to deciphering the role of frequently occurring SMARCA4 alterations in Group 3 medulloblastoma with the perspective to explore targeted therapeutic options.
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Affiliation(s)
- Carolin Göbel
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany
| | - Shweta Godbole
- Center for Molecular Neurobiology, Falkenried 94, Hamburg, 20251, Germany
| | - Melanie Schoof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany
| | - Dörthe Holdhof
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany
| | - Catena Kresbach
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
| | - Carolin Loose
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany
| | - Julia Neumann
- Center for Molecular Neurobiology, Falkenried 94, Hamburg, 20251, Germany
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany
| | - Ulrich Schüller
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany.
- Research Institute Children's Cancer Center Hamburg, Martinistrasse 52, Building N63 (LIV), Hamburg, D-20251, Germany.
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, Hamburg, 20251, Germany.
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6
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Ye J, Liu W, Yu X, Wu L, Chen Z, Yu Y, Wang J, Bai S, Zhang M. TRAF7-targeted HOXA5 acts as a tumor suppressor in prostate cancer progression and stemness via transcriptionally activating SPRY2 and regulating MEK/ERK signaling. Cell Death Discov 2023; 9:378. [PMID: 37845209 PMCID: PMC10579307 DOI: 10.1038/s41420-023-01675-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/23/2023] [Accepted: 10/03/2023] [Indexed: 10/18/2023] Open
Abstract
Homeobox A5 (HOXA5), a homeodomain transcription factor, is considered a tumor suppressor in cancer progression; however, its function in prostate cancer (PCa) remains unclear. This study focused on the relevance of HOXA5 in PCa progression. We identified the downregulation of HOXA5 in PCa tissues based on the TCGA database and further verified in 30-paired PCa and adjacent normal tissues. Functional studies revealed that HOXA5 upregulation impaired the stem-like characteristics and malignant behaviors of PCa cells in vitro and in vivo. Mechanistically, HOXA5 was found to be regulated by tumor necrosis factor receptor-associated factor 7 (TRAF7), a putative E3-ubiquitin ligase. We observed that TRAF7 was overexpressed in PCa and subsequently enhanced the degradation of HOXA5 protein via its ubiquitin ligase activity, contributing to the acquisition of an aggressive PCa phenotype. For its downstream mechanism, we demonstrated that sprouty RTK signaling antagonist 2 (SPRY2) served as a downstream target of HOXA5. HOXA5 could directly bind to the SPRY2 promoter, thereby regulating the SPRY2-mediated MEK/ERK signaling pathway. Silencing SPRY2 largely compromised the tumor-suppressive effect of HOXA5 in PCa progression and cancer stemness. Our findings highlight the previously-underappreciated signaling axis of TRAF7-HOXA5-SPRY2, which provides a novel prognostic and therapeutic target for PCa treatment.
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Affiliation(s)
- Jianfeng Ye
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Wangmin Liu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Xueyang Yu
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Lina Wu
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China
| | - Zhengjie Chen
- Department of Urology, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yufei Yu
- Department of Urology, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jianfeng Wang
- Department of Urology, the First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Song Bai
- Department of Urology, Shengjing Hospital of China Medical University, Shenyang, Liaoning, China.
| | - Mo Zhang
- Department of Urology, the First Hospital of China Medical University, Shenyang, Liaoning, China.
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7
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Machado GC, Ferrer VP. MUC17 mutations and methylation are associated with poor prognosis in adult-type diffuse glioma patients. J Neurol Sci 2023; 452:120762. [PMID: 37562166 DOI: 10.1016/j.jns.2023.120762] [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: 02/10/2023] [Revised: 07/03/2023] [Accepted: 07/31/2023] [Indexed: 08/12/2023]
Abstract
Diffuse gliomas are tumors that arise from glial or glial progenitor cells. They are currently classified as astrocytoma isocitrate dehydrogenase (IDH)-mutant or oligodendroglioma IDH-mutant, and 1p/19q-codeleted, both slower-growing tumors, or glioblastoma (GBM), a more aggressive tumor. Despite advances in the diagnosis and treatment of gliomas, the median survival time after diagnosis of GBM remains low, approximately 15 months, with a 5-year overall survival rate of only 6.8%. Therefore, new biomarkers that could support the earlier diagnosis and prognosis of these tumors would be of great value. MUC17, a membrane-bound mucin, has been identified as a potential biomarker for several tumors. However, the role of this mucin in adult gliomas has not yet been explored. Here, we show for the first time, in a retrospective study and by in silico analysis that MUC17 is one of the relevant mutant genes in adult gliomas. Moreover, that an increase in MUC17 methylation correlates with an increase in glioma malignancy grade. Patients with MUC17 mutations had a poorer prognosis than their wild-type counterparts in both GBM and non-GBM glioma cohorts. We also analyzed mutational profiles that correlated strongly with poor survival. Therefore, in this study, we present a new potential biomarker for further investigation, especially for the prognosis of adult diffuse gliomas.
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Affiliation(s)
- Gabriel Cardoso Machado
- Laboratory of Cell and Molecular Biology of Tumors, Department of Cell and Molecular Biology, Biology Institute, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil; Graduate Program in Pathological Anatomy, Faculty of Medicine, Rio de Janeiro Federal University, Rio de Janeiro, Brazil
| | - Valéria Pereira Ferrer
- Laboratory of Cell and Molecular Biology of Tumors, Department of Cell and Molecular Biology, Biology Institute, Fluminense Federal University, Niterói, Rio de Janeiro, Brazil; Graduate Program in Pathological Anatomy, Faculty of Medicine, Rio de Janeiro Federal University, Rio de Janeiro, Brazil.
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8
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Parrillo L, Spinelli R, Longo M, Zatterale F, Santamaria G, Leone A, Campitelli M, Raciti GA, Beguinot F. The Transcription Factor HOXA5: Novel Insights into Metabolic Diseases and Adipose Tissue Dysfunction. Cells 2023; 12:2090. [PMID: 37626900 PMCID: PMC10453582 DOI: 10.3390/cells12162090] [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: 06/15/2023] [Revised: 08/03/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023] Open
Abstract
The transcription factor HOXA5, from the HOX gene family, has long been studied due to its critical role in physiological activities in normal cells, such as organ development and body patterning, and pathological activities in cancer cells. Nonetheless, recent evidence supports the hypothesis of a role for HOXA5 in metabolic diseases, particularly in obesity and type 2 diabetes (T2D). In line with the current opinion that adipocyte and adipose tissue (AT) dysfunction belong to the group of primary defects in obesity, linking this condition to an increased risk of insulin resistance (IR) and T2D, the HOXA5 gene has been shown to regulate adipocyte function and AT remodeling both in humans and mice. Epigenetics adds complexity to HOXA5 gene regulation in metabolic diseases. Indeed, epigenetic mechanisms, specifically DNA methylation, influence the dynamic HOXA5 expression profile. In human AT, the DNA methylation profile at the HOXA5 gene is associated with hypertrophic obesity and an increased risk of developing T2D. Thus, an inappropriate HOXA5 gene expression may be a mechanism causing or maintaining an impaired AT function in obesity and potentially linking obesity to its associated disorders. In this review, we integrate the current evidence about the involvement of HOXA5 in regulating AT function, as well as its association with the pathogenesis of obesity and T2D. We also summarize the current knowledge on the role of DNA methylation in controlling HOXA5 expression. Moreover, considering the susceptibility of epigenetic changes to reversal through targeted interventions, we discuss the potential therapeutic value of targeting HOXA5 DNA methylation changes in the treatment of metabolic diseases.
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Affiliation(s)
- Luca Parrillo
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Rosa Spinelli
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
- Lundberg Laboratory for Diabetes Research, Department of Molecular and Clinical Medicine, Sahlgrenska Academy, University of Gothenburg, 41345 Gothenburg, Sweden
| | - Michele Longo
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Federica Zatterale
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Gianluca Santamaria
- Department of Experimental and Clinical Medicine, University Magna Græcia of Catanzaro, 88100 Catanzaro, Italy;
| | - Alessia Leone
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Michele Campitelli
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Gregory Alexander Raciti
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
| | - Francesco Beguinot
- URT Genomics of Diabetes, Institute of Experimental Endocrinology and Oncology, National Research Council, Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy; (R.S.); (M.L.); (F.Z.); (A.L.); (M.C.); (G.A.R.)
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9
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Wang Y, Wang Y, Liu B, Gao X, Li Y, Li F, Zhou H. Mapping the tumor microenvironment in clear cell renal carcinoma by single-cell transcriptome analysis. Front Genet 2023; 14:1207233. [PMID: 37533434 PMCID: PMC10392130 DOI: 10.3389/fgene.2023.1207233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 07/06/2023] [Indexed: 08/04/2023] Open
Abstract
Introduction: Clear cell renal cell carcinoma (ccRCC) is associated with unfavorable clinical outcomes. To identify viable therapeutic targets, a comprehensive understanding of intratumoral heterogeneity is crucial. In this study, we conducted bioinformatic analysis to scrutinize single-cell RNA sequencing data of ccRCC tumor and para-tumor samples, aiming to elucidate the intratumoral heterogeneity in the ccRCC tumor microenvironment (TME). Methods: A total of 51,780 single cells from seven ccRCC tumors and five para-tumor samples were identified and grouped into 11 cell lineages using bioinformatic analysis. These lineages included tumor cells, myeloid cells, T-cells, fibroblasts, and endothelial cells, indicating a high degree of heterogeneity in the TME. Copy number variation (CNV) analysis was performed to compare CNV frequencies between tumor and normal cells. The myeloid cell population was further re-clustered into three major subgroups: monocytes, macrophages, and dendritic cells. Differential expression analysis, gene ontology, and gene set enrichment analysis were employed to assess inter-cluster and intra-cluster functional heterogeneity within the ccRCC TME. Results: Our findings revealed that immune cells in the TME predominantly adopted an inflammatory suppression state, promoting tumor cell growth and immune evasion. Additionally, tumor cells exhibited higher CNV frequencies compared to normal cells. The myeloid cell subgroups demonstrated distinct functional properties, with monocytes, macrophages, and dendritic cells displaying diverse roles in the TME. Certain immune cells exhibited pro-tumor and immunosuppressive effects, while others demonstrated antitumor and immunostimulatory properties. Conclusion: This study contributes to the understanding of intratumoral heterogeneity in the ccRCC TME and provides potential therapeutic targets for ccRCC treatment. The findings emphasize the importance of considering the diverse functional roles of immune cells in the TME for effective therapeutic interventions.
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Affiliation(s)
- Yuxiong Wang
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Yishu Wang
- Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Jilin, China
| | - Bin Liu
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Xin Gao
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Yunkuo Li
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Faping Li
- Department of Urology, The First Hospital of Jilin University, Jilin, China
| | - Honglan Zhou
- Department of Urology, The First Hospital of Jilin University, Jilin, China
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10
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Zheng ZQ, Yuan GQ, Zhang GG, Nie QQ, Wang Z. Development and validation of a predictive model in diagnosis and prognosis of primary glioblastoma patients based on Homeobox A family. Discov Oncol 2023; 14:108. [PMID: 37351805 DOI: 10.1007/s12672-023-00726-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 06/13/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Homeobox A (HOXA) family is involved in the development of malignancies as either tumor suppressors or oncogenes. However, their roles in glioblastoma (GBM) and clinical significance have not been fully elucidated. METHODS HOXA mutation and expressions in pan-cancers were investigated using GSCA and Oncomine, which in GBM were validated by cBioPortal, Chinese Glioma Genome Atlas (CGGA), and The Cancer Genome Atlas (TCGA) datasets. Kaplan-Meier analyses were conducted to determine prognostic values of HOXAs at genetic and mRNA levels. Diagnostic roles of HOXAs in tumor classification were explored by GlioVis and R software. Independent prognostic HOXAs were identified using Cox survival analyses, the least absolute shrinkage and selection operator (LASSO) regression, quantitative real-time PCR, and immunohistochemical staining. A HOXAs-based nomogram survival prediction model was developed and evaluated using Kaplan-Meier analysis, time-dependent Area Under Curve, calibration plots, and Decision Curve Analysis in training and validation cohorts. RESULTS HOXAs were highly mutated and overexpressed in pan-cancers, especially in CGGA and TCGA GBM datasets. Genetic alteration and mRNA expression of HOXAs were both found to be prognostic. Specific HOXAs could distinguish IDH mutation (HOXA1-7, HOXA9, HOXA13) and molecular GBM subtypes (HOXA1-2, HOXA9-11, HOXA13). HOXA1/2/3/10 were confirmed to be independent prognostic members, with high expressions validated in clinical GBM tissues. The HOXAs-based nomogram model exhibited good prediction performance and net benefits for patients in training and validation cohorts. CONCLUSION HOXA family has diagnostic values, and the HOXAs-based nomogram model is effective in survival prediction, providing a novel approach to support the treatment of GBM patients.
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Affiliation(s)
- Zong-Qing Zheng
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu Province, China
| | - Gui-Qiang Yuan
- Beijing Neurosurgical Institute & Department of Neurosurgery, Beijing Tiantan Hospital Affiliated to Capital Medical University, Capital Medical University, Beijing, China
| | - Guo-Guo Zhang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu Province, China
| | - Qian-Qian Nie
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu Province, China
| | - Zhong Wang
- Department of Neurosurgery & Brain and Nerve Research Laboratory, The First Affiliated Hospital of Soochow University, 188 Shizi Street, Suzhou, 215006, Jiangsu Province, China.
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11
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Wang JZ, Nassiri F, Aldape K, von Deimling A, Sahm F. The Epigenetic Landscape of Meningiomas. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1416:175-188. [PMID: 37432627 DOI: 10.1007/978-3-031-29750-2_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Epigenetic changes have been found to be increasingly important in tumor development and progression. These alterations can be present in tumors such as meningiomas in the absence of any gene mutations and alter gene expression without affecting the sequence of the DNA itself. Some examples of these alterations that have been studied in meningiomas include DNA methylation, microRNA interaction, histone packaging, and chromatin restructuring. In this chapter we will describe in detail each of these mechanisms of epigenetic modification in meningiomas and their prognostic significance.
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Affiliation(s)
- Justin Z Wang
- Division of Neurosurgery, Department of Surgery, The University of Toronto, Toronto, ON, Canada
| | - Farshad Nassiri
- Division of Neurosurgery, Department of Surgery, The University of Toronto, Toronto, ON, Canada.
| | - Kenneth Aldape
- Laboratory of Pathology, Center Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Andreas von Deimling
- CCU Neuropathology, German Cancer Research Center (DKFZ), University Heidelberg, Heidelberg, Germany
| | - Felix Sahm
- CCU Neuropathology, German Cancer Research Center (DKFZ), University Heidelberg, Heidelberg, Germany
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12
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Abdallah AS, Cardona HJ, Gadd SL, Brat DJ, Powla PP, Alruwalli WS, Shen C, Picketts DJ, Li XN, Becher OJ. Novel genetically engineered H3.3G34R model reveals cooperation with ATRX loss in upregulation of Hoxa cluster genes and promotion of neuronal lineage. Neurooncol Adv 2023; 5:vdad003. [PMID: 36845293 PMCID: PMC9950856 DOI: 10.1093/noajnl/vdad003] [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] [Indexed: 01/09/2023] Open
Abstract
Background Pediatric high-grade gliomas (pHGGs) are aggressive pediatric CNS tumors and an important subset are characterized by mutations in H3F3A, the gene that encodes Histone H3.3 (H3.3). Substitution of Glycine at position 34 of H3.3 with either Arginine or Valine (H3.3G34R/V), was recently described and characterized in a large cohort of pHGG samples as occurring in 5-20% of pHGGs. Attempts to study the mechanism of H3.3G34R have proven difficult due to the lack of knowledge regarding the cell-of-origin and the requirement for co-occurring mutations for model development. We sought to develop a biologically relevant animal model of pHGG to probe the downstream effects of the H3.3G34R mutation in the context of vital co-occurring mutations. Methods We developed a genetically engineered mouse model (GEMM) that incorporates PDGF-A activation, TP53 loss and the H3.3G34R mutation both in the presence and loss of Alpha thalassemia/mental retardation syndrome X-linked (ATRX), which is commonly mutated in H3.3G34 mutant pHGGs. Results We demonstrated that ATRX loss significantly increases tumor latency in the absence of H3.3G34R and inhibits ependymal differentiation in the presence of H3.3G34R. Transcriptomic analysis revealed that ATRX loss in the context of H3.3G34R upregulates Hoxa cluster genes. We also found that the H3.3G34R overexpression leads to enrichment of neuronal markers but only in the context of ATRX loss. Conclusions This study proposes a mechanism in which ATRX loss is the major contributor to many key transcriptomic changes in H3.3G34R pHGGs. Accession number GSE197988.
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Affiliation(s)
- Aalaa S Abdallah
- Department of Pediatrics, Northwestern University, Chicago, Illinois, USA
- Stanley Manne Children’s Research Institute, Molecular and Translational Cancer Biology, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Herminio J Cardona
- Stanley Manne Children’s Research Institute, Molecular and Translational Cancer Biology, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Samantha L Gadd
- Department of Pathology, Northwestern University, Chicago, Illinois, USA
| | - Daniel J Brat
- Department of Pathology, Northwestern University, Chicago, Illinois, USA
| | - Plamena P Powla
- Department of Psychiatry and Behavioral Sciences, Northwestern University, Chicago, Illinois, USA
| | - Waleed S Alruwalli
- Department of Psychiatry and Behavioral Sciences, Northwestern University, Chicago, Illinois, USA
| | - Chen Shen
- Stanley Manne Children’s Research Institute, Molecular and Translational Cancer Biology, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - David J Picketts
- Regenerative Medicine Program, Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | - Xiao-Nan Li
- Department of Pediatrics, Northwestern University, Chicago, Illinois, USA
- Stanley Manne Children’s Research Institute, Molecular and Translational Cancer Biology, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
- Developmental Therapeutic Core, Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Program of Precision Medicine PDOX Modeling of Pediatric Tumors, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Oren J Becher
- Department of Pediatrics, Northwestern University, Chicago, Illinois, USA
- Stanley Manne Children’s Research Institute, Molecular and Translational Cancer Biology, Ann & Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Kravis Children’s Hospital, Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Department of Oncological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA
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13
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HOXA5: A crucial transcriptional factor in cancer and a potential therapeutic target. Biomed Pharmacother 2022; 155:113800. [DOI: 10.1016/j.biopha.2022.113800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/29/2022] [Accepted: 10/02/2022] [Indexed: 11/20/2022] Open
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Le Boiteux E, Guichet PO, Masliantsev K, Montibus B, Vaurs-Barriere C, Gonthier-Gueret C, Chautard E, Verrelle P, Karayan-Tapon L, Fogli A, Court F, Arnaud P. The Long Non-Coding RNA HOXA-AS2 Promotes Proliferation of Glioma Stem Cells and Modulates Their Inflammation Pathway Mainly through Post-Transcriptional Regulation. Int J Mol Sci 2022; 23:ijms23094743. [PMID: 35563134 PMCID: PMC9102906 DOI: 10.3390/ijms23094743] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/15/2022] [Accepted: 04/22/2022] [Indexed: 12/21/2022] Open
Abstract
Glioblastomas represent approximatively half of all gliomas and are the most deadly and aggressive form. Their therapeutic resistance and tumor relapse rely on a subpopulation of cells that are called Glioma Stem Cells (GSCs). Here, we investigated the role of the long non-coding RNA HOXA-AS2 in GSC biology using descriptive and functional analyses of glioma samples classified according to their isocitrate dehydrogenase (IDH) gene mutation status, and of GSC lines. We found that HOXA-AS2 is overexpressed only in aggressive (IDHwt) glioma and GSC lines. ShRNA-based depletion of HOXA-AS2 in GSCs decreased cell proliferation and altered the expression of several hundreds of genes. Integrative analysis revealed that these expression changes were not associated with changes in DNA methylation or chromatin signatures at the promoter of the majority of genes deregulated following HOXA-AS2 silencing in GSCs, suggesting a post-transcriptional regulation. In addition, transcription factor binding motif enrichment and correlation analyses indicated that HOXA-AS2 affects, directly or indirectly, the expression of key transcription factors implicated in GCS biology, including E2F8, E2F1, STAT1, and ATF3, thus contributing to GCS aggressiveness by promoting their proliferation and modulating the inflammation pathway.
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Affiliation(s)
- Elisa Le Boiteux
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Pierre-Olivier Guichet
- ProDiCeT UR 24144, Université de Poitiers, F-86000 Poitiers, France; (P.-O.G.); (K.M.); (L.K.-T.)
- Laboratoire de Cancérologie Biologique, CHU de Poitiers, F-86000 Poitiers, France
| | - Konstantin Masliantsev
- ProDiCeT UR 24144, Université de Poitiers, F-86000 Poitiers, France; (P.-O.G.); (K.M.); (L.K.-T.)
- Laboratoire de Cancérologie Biologique, CHU de Poitiers, F-86000 Poitiers, France
| | - Bertille Montibus
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Catherine Vaurs-Barriere
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Céline Gonthier-Gueret
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
| | - Emmanuel Chautard
- Pathology Department, Jean Perrin Center, F-63000 Clermont-Ferrand, France;
- INSERM, U1240 IMoST, Université Clermont Auvergne, F-63000 Clermont-Ferrand, France
| | - Pierre Verrelle
- CIMB, INSERM U1196 CNRS UMR9187, Curie Institute, F-91400 Orsay, France;
- Radiotherapy Department, Curie Institute, F-75248 Paris, France
- CNRS UMR 9187, INSERM U1196, Institut Curie, PSL Research University and Paris-Saclay University, F-91405 Orsay, France
| | - Lucie Karayan-Tapon
- ProDiCeT UR 24144, Université de Poitiers, F-86000 Poitiers, France; (P.-O.G.); (K.M.); (L.K.-T.)
- Laboratoire de Cancérologie Biologique, CHU de Poitiers, F-86000 Poitiers, France
| | - Anne Fogli
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
- Radiation Oncology Department, Institut Curie, F-75005 Paris, France
| | - Franck Court
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
- Correspondence: (F.C.); (P.A.)
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, Inserm, GReD, F-63000 Clermont-Ferrand, France; (E.L.B.); (B.M.); (C.V.-B.); (C.G.-G.); (A.F.)
- Correspondence: (F.C.); (P.A.)
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15
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Yang Q, Jiang N, Zou H, Fan X, Liu T, Huang X, Wanggou S, Li X. Alterations in 3D chromatin organization contribute to tumorigenesis of EGFR-amplified glioblastoma. Comput Struct Biotechnol J 2022; 20:1967-1978. [PMID: 35521558 PMCID: PMC9062087 DOI: 10.1016/j.csbj.2022.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/05/2022] [Accepted: 04/05/2022] [Indexed: 02/06/2023] Open
Abstract
There is widespread chromatin disorganization in EGFR-amplified glioblastoma. Chromatin disorganization contribute to tumorigenesis in glioblastoma. Structural variations have a substantial impact on chromatin conformation.
Background EGFR amplification and/or mutation are found in more than half of the cases with glioblastoma. Yet, the role of chromatin interactions and its regulation of gene expression in EGFR-amplified glioblastoma remains unclear. Methods In this study, we explored alterations in 3D chromatin organization of EGFR-amplified glioblastoma and its subsequent impact by performing a comparative analysis of Hi-C, RNA-seq, and whole-genome sequencing (WGS) on EGFR-amplified glioblastoma-derived A172 and normal astrocytes (HA1800 cell line). Results A172 cells showed an elevated chromatin relaxation, and unexpected entanglement of chromosome regions. A genome-wide landscape of switched compartments and differentially expressed genes between HA1800 and A172 cell lines demonstrated that compartment activation reshaped chromatin accessibility and activated tumorigenesis-related genes. Topological associating domain (TAD) analysis revealed that altered TAD domains in A172 also contribute to oncogene activation and tumor repressor deactivation. Interestingly, glioblastoma-derived A172 cells showed a different chromatin loop contact propensity. Genes in tumorigenesis-associated signaling pathways were significantly enriched at the anchor loci of altered chromatin loops. Oncogene activation and tumor repressor deactivation were associated with chromatin loop alteration. Structure variations (SVs) had a dramatic impact on the chromatin conformation of EGFR-amplified glioblastoma-derived tumor cells. Moreover, our results revealed that 7p11.2 duplication activated EGFR expression in EGFR-amplified glioblastoma via neo-TAD formation and novel enhancer-promoter interaction emergence between LINC01446 and EGFR. Conclusions The disordered 3D genomic map and multi-omics data of EGFR-amplified glioblastoma provide a resource for future interrogation of the relationship between chromatin interactions and transcriptome in tumorigenesis.
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Affiliation(s)
- Qi Yang
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, Hunan 410008, PR China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, Hunan 410008, PR China
| | - Nian Jiang
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, Hunan 410008, PR China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, Hunan 410008, PR China
| | - Han Zou
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, Hunan 410008, PR China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, Hunan 410008, PR China
| | - Xuning Fan
- Annoroad Gene Tech. (Beijing) Co., Ltd, Block 1, Yard 88, Kechuang 6 RD, Beijing Economic-Technological Development Area, Beijing 100176, PR China
| | - Tao Liu
- Annoroad Gene Tech. (Beijing) Co., Ltd, Block 1, Yard 88, Kechuang 6 RD, Beijing Economic-Technological Development Area, Beijing 100176, PR China
| | - Xi Huang
- Program in Developmental and Stem Cell Biology, The Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
- Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, M5S 3E1, Canada
| | - Siyi Wanggou
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, Hunan 410008, PR China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, Hunan 410008, PR China
- Corresponding authors at: Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China.
| | - Xuejun Li
- Department of Neurosurgery, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, Hunan 410008, PR China
- Hunan International Scientific and Technological Cooperation Base of Brain Tumor Research, Xiangya Hospital, Central South University, No. 87, Xiangya Road, Changsha, Hunan 410008, PR China
- Corresponding authors at: Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, PR China.
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Wang J, Chen Y, Wang Q, Xu H, Wu C, Jiang Q, Wu G, Zhou H, Xiao Z, Chen Y, Zhang T, Lan Q. MEOX2-mediated regulation of Cathepsin S promotes cell proliferation and motility in glioma. Cell Death Dis 2022; 13:360. [PMID: 35436995 PMCID: PMC9016080 DOI: 10.1038/s41419-022-04845-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/01/2022] [Accepted: 04/06/2022] [Indexed: 11/30/2022]
Abstract
Nuclear transcription factor Mesenchyme Homeobox 2 (MEOX2) is a homeobox gene that is originally discovered to suppress the growth of vascular smooth muscle and endothelial cells. However, whether or not it is connected to cancer is yet unknown. Here, we report that MEOX2 functions as a tumor-initiating element in glioma. Bioinformatic analyses of public databases and investigation of MEOX2 expression in patients with glioma demonstrated that MEOX2 was abundant at both mRNA and protein levels in glioma. MEOX2 expression was shown to be inversely linked with the prognosis of glioma patients. MEOX2 inhibition changed the morphology of glioma cells, inhibited cell proliferation and motility, whereas had no effect on cell apoptosis. Besides, silencing MEOX2 also hampered the epithelial-mesenchymal transition (EMT), focal adhesion formation, and F-actin assembly. Overexpression of MEOX2 exhibited opposite effects. Importantly, RNA-sequencing, ChIP-qPCR assay, and luciferase reporter assay revealed Cathepsin S (CTSS) as a novel transcriptional target of MEOX2 in glioma cells. Consistently, MEOX2 causes glioma tumor development in mice and greatly lowers the survival period of tumor-bearing mice. Our findings indicate that MEOX2 promotes tumorigenesis and progression of glioma partially through the regulation of CTSS. Targeting MEOX2-CTSS axis might be a promising alternative for the treatment of glioma.
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He ZC, Liu Q, Yang KD, Chen C, Zhang XN, Wang WY, Zeng H, Wang B, Liu YQ, Luo M, Li L, Niu Q, Lu HM, Luo T, Yao XH, Guo HT, Ji JL, Cao MF, Shi Y, Ping YF, Bian XW. HOXA5 is amplified in glioblastoma stem cells and promotes tumor progression by transcriptionally activating PTPRZ1. Cancer Lett 2022; 533:215605. [DOI: 10.1016/j.canlet.2022.215605] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 01/23/2023]
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18
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Morgan R, Hunter K, Pandha HS. Downstream of the HOX genes: explaining conflicting tumour suppressor and oncogenic functions in cancer. Int J Cancer 2022; 150:1919-1932. [PMID: 35080776 PMCID: PMC9304284 DOI: 10.1002/ijc.33949] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/24/2021] [Accepted: 01/07/2022] [Indexed: 11/07/2022]
Abstract
The HOX genes are a highly conserved group of transcription factors that have key roles in early development, but which are also highly expressed in most cancers. Many studies have found strong associative relationships between the expression of individual HOX genes in tumours and clinical parameters including survival. For the majority of HOX genes, high tumour expression levels seem to be associated with a worse outcome for patients, and in some cases this has been shown to result from the activation of pro-oncogenic genes and pathways. However, there are also many studies that indicate a tumour suppressor role for some HOX genes, sometimes with conclusions that contradict earlier work. In this review, we have attempted to clarify the role of HOX genes in cancer by focusing on their downstream targets as identified in studies that provide experimental evidence for their activation or repression. On this basis, the majority of HOX genes would appear to have a pro-oncogenic function, with the notable exception of HOXD10, which acts exclusively as a tumour suppressor. HOX proteins regulate a wide range of target genes involved in metastasis, cell death, proliferation, and angiogenesis, and activate key cell signalling pathways. Furthermore, for some functionally related targets, this regulation is achieved by a relatively small subgroup of HOX genes.
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Affiliation(s)
- Richard Morgan
- School of Biomedical SciencesUniversity of West LondonLondonUK
| | - Keith Hunter
- Unit of Oral and Maxillofacial Pathology, School of Clinical DentistryUniversity of SheffieldSheffieldUK
| | - Hardev S. Pandha
- Faculty of Health and Medical SciencesUniversity of SurreyGuildfordUK
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19
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Schönrock A, Heinzelmann E, Steffl B, Demirdizen E, Narayanan A, Krunic D, Bähr M, Park JW, Schmidt C, Özduman K, Pamir MN, Wick W, Bestvater F, Weichenhan D, Plass C, Taranda J, Mall M, Turcan Ş. OUP accepted manuscript. Neuro Oncol 2022; 24:1911-1924. [PMID: 35468210 PMCID: PMC9629421 DOI: 10.1093/neuonc/noac110] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Glioblastoma (GBM) is an aggressive tumor that frequently exhibits gain of chromosome 7, loss of chromosome 10, and aberrantly activated receptor tyrosine kinase signaling pathways. Previously, we identified Mesenchyme Homeobox 2 (MEOX2), a gene located on chromosome 7, as an upregulated transcription factor in GBM. Overexpressed transcription factors can be involved in driving GBM. Here, we aimed to address the role of MEOX2 in GBM. METHODS Patient-derived GBM tumorspheres were used to constitutively knockdown or overexpress MEOX2 and subjected to in vitro assays including western blot to assess ERK phosphorylation. Cerebral organoid models were used to investigate the role of MEOX2 in growth initiation. Intracranial mouse implantation models were used to assess the tumorigenic potential of MEOX2. RNA-sequencing, ACT-seq, and CUT&Tag were used to identify MEOX2 target genes. RESULTS MEOX2 enhanced ERK signaling through a feed-forward mechanism. We identified Ser155 as a putative ERK-dependent phosphorylation site upstream of the homeobox-domain of MEOX2. S155A substitution had a major effect on MEOX2 protein levels and altered its subnuclear localization. MEOX2 overexpression cooperated with p53 and PTEN loss in cerebral organoid models of human malignant gliomas to induce cell proliferation. Using high-throughput genomics, we identified putative transcriptional target genes of MEOX2 in patient-derived GBM tumorsphere models and a fresh frozen GBM tumor. CONCLUSIONS We identified MEOX2 as an oncogenic transcription regulator in GBM. MEOX2 increases proliferation in cerebral organoid models of GBM and feeds into ERK signaling that represents a core signaling pathway in GBM.
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Affiliation(s)
| | | | | | | | - Ashwin Narayanan
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Damir Krunic
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marion Bähr
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Claudia Schmidt
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Koray Özduman
- Department of Neurosurgery, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - M Necmettin Pamir
- Department of Neurosurgery, School of Medicine, Acibadem Mehmet Ali Aydinlar University, Istanbul, Turkey
| | - Wolfgang Wick
- Clinical Cooperation Unit Neurooncology, German Consortium for Translational Cancer Research (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Bestvater
- Core Facility Unit Light Microscopy, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Weichenhan
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Christoph Plass
- Division of Cancer Epigenomics, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Julian Taranda
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Moritz Mall
- Cell Fate Engineering and Disease Modeling Group, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, Heidelberg, Germany
- HITBR Hector Institute for Translational Brain Research gGmbH, Heidelberg, Germany
- Central Institute of Mental Health, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Şevin Turcan
- Corresponding Author: Şevin Turcan, PhD, Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, INF 460, Heidelberg, Germany ()
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20
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Ding F, Chen P, Bie P, Piao W, Cheng Q. HOXA5 Is Recognized as a Prognostic-Related Biomarker and Promotes Glioma Progression Through Affecting Cell Cycle. Front Oncol 2021; 11:633430. [PMID: 34485110 PMCID: PMC8416157 DOI: 10.3389/fonc.2021.633430] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 07/19/2021] [Indexed: 11/13/2022] Open
Abstract
Glioma is malignant tumor derives from glial cells in the central nervous system. High-grade glioma shows aggressive growth pattern, and conventional treatments, such as surgical removal and chemo-radiotherapy, archive limitation in the interference of this process. In this work, HOXA5, from the HOX family, was identified as a glioma cell proliferation-associated factor by investigating its feature in the TCGA and CGGA data set. High HOXA5 expression samples contain unfavorable clinical features of glioma, including IDH wild type, un-methylated MGMT status, non-codeletion 1p19q status, malignant molecular subtype. Survival analysis indicates that high HOXA5 expression samples are associated with worse clinical outcome. The CNVs and SNPs profile difference further confirmed the enrichment of glioma aggressive related biomarkers. In the meantime, the activation of DNA damage repair-related pathways and TP53-related pathways is also related to HOXA5 expression. In cell lines, U87MG and U251, by interfering HOXA5 expression significantly inhibit glioma progression and apoptosis, and cell cycle is arrested at the G2/M phase. Collectively, increased HOXA5 expression can promote glioma progression via affecting glioma cell proliferation.
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Affiliation(s)
- Fengqin Ding
- Department of Clinical Laboratory, People's Hospital of Ningxia Hui Autonomous Region, First Affiliated Hospital of Northwest Minzu University, Yinchuan, China
| | - Ping Chen
- Medical Experiment Center, General Hospital of Ningxia Medical University, Yinchuan, China
| | - Pengfei Bie
- Department of Neurosurgery, People's Hospital of Ningxia Hui Autonomous Region, First Affiliated Hospital of Northwest Minzu University, Yinchuan, China
| | - Wenhua Piao
- Department of Clinical Laboratory, People's Hospital of Ningxia Hui Autonomous Region, First Affiliated Hospital of Northwest Minzu University, Yinchuan, China
| | - Quan Cheng
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China.,National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.,Clinical Diagnosis and Therapy Center for Glioma of Xiangya Hospital, Central South University, Changsha, China.,Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
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21
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Sharanek A, Burban A, Hernandez-Corchado A, Madrigal A, Fatakdawala I, Najafabadi HS, Soleimani VD, Jahani-Asl A. Transcriptional control of brain tumor stem cells by a carbohydrate binding protein. Cell Rep 2021; 36:109647. [PMID: 34469737 DOI: 10.1016/j.celrep.2021.109647] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/29/2021] [Accepted: 08/09/2021] [Indexed: 12/12/2022] Open
Abstract
Brain tumor stem cells (BTSCs) and intratumoral heterogeneity represent major challenges in glioblastoma therapy. Here, we report that the LGALS1 gene, encoding the carbohydrate binding protein, galectin1, is a key regulator of BTSCs and glioblastoma resistance to therapy. Genetic deletion of LGALS1 alters BTSC gene expression profiles and results in downregulation of gene sets associated with the mesenchymal subtype of glioblastoma. Using a combination of pharmacological and genetic approaches, we establish that inhibition of LGALS1 signaling in BTSCs impairs self-renewal, suppresses tumorigenesis, prolongs lifespan, and improves glioblastoma response to ionizing radiation in preclinical animal models. Mechanistically, we show that LGALS1 is a direct transcriptional target of STAT3 with its expression robustly regulated by the ligand OSM. Importantly, we establish that galectin1 forms a complex with the transcription factor HOXA5 to reprogram the BTSC transcriptional landscape. Our data unravel an oncogenic signaling pathway by which the galectin1/HOXA5 complex maintains BTSCs and promotes glioblastoma.
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Affiliation(s)
- Ahmad Sharanek
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Gerald Bronfman Department of Oncology and Division of Experimental Medicine, McGill University, Montréal, QC H4A 3T2, Canada
| | - Audrey Burban
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Gerald Bronfman Department of Oncology and Division of Experimental Medicine, McGill University, Montréal, QC H4A 3T2, Canada
| | - Aldo Hernandez-Corchado
- Department of Human Genetics, McGill University, Montréal, QC H3A OC7, Canada; McGill Genome Centre, Montréal, QC H3A 0G1, Canada
| | - Ariel Madrigal
- Department of Human Genetics, McGill University, Montréal, QC H3A OC7, Canada; McGill Genome Centre, Montréal, QC H3A 0G1, Canada
| | - Idris Fatakdawala
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T 1E2, Canada
| | - Hamed S Najafabadi
- Department of Human Genetics, McGill University, Montréal, QC H3A OC7, Canada; McGill Genome Centre, Montréal, QC H3A 0G1, Canada
| | - Vahab D Soleimani
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Department of Human Genetics, McGill University, Montréal, QC H3A OC7, Canada
| | - Arezu Jahani-Asl
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montréal, QC H3T 1E2, Canada; Gerald Bronfman Department of Oncology and Division of Experimental Medicine, McGill University, Montréal, QC H4A 3T2, Canada; Integrated program in Neuroscience, Montréal Neurological Institute, Montréal, QC H3A 2B4, Canada.
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22
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A comprehensive prognostic signature for glioblastoma patients based on transcriptomics and single cell sequencing. Cell Oncol (Dordr) 2021; 44:917-935. [PMID: 34142341 DOI: 10.1007/s13402-021-00612-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 05/17/2021] [Indexed: 10/21/2022] Open
Abstract
PURPOSE Glioblastoma (GBM) is the most common and deadly brain tumor. We aimed to reveal potential prognostic GBM marker genes, elaborate their functions, and build an effective a prognostic model for GBM patients. METHODS Through data mining of The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA), we screened for significantly differentially expressed genes (DEGs) to calculate risk scores for individual patients. Published data of somatic mutation and copy number variation profiles were analyzed for distinct genomic alterations associated with risk scores. In addition, single-cell sequencing was used to explore the biological functions of the identified prognostic marker genes. By combining risk scores and other clinical features, we built a comprehensive prognostic GBM model. RESULTS Seven DEGs (CLEC5A, HOXC6, HOXA5, CCL2, GPRASP1, BSCL2 and PTX3) were identified as being prognostic for GBM. Expression of these genes was confirmed in different GBM cell lines using real-time PCR. Risk scores calculated from the seven DEGs revealed prognostic value irrespective of other clinical factors, including IDH mutation status, and were negatively correlated with TP53 expression. The prognostic genes were found to be associated with tumor proliferation and progression based on pseudo-time analysis in neoplastic cells. A final prognostic model was developed and validated with a good performance, especially in geriatric GBM patients. CONCLUSIONS Using genetic profiles, age, IDH mutation status, and chemotherapy and radiotherapy, we constructed a comprehensive prognostic model for GBM patients. The model has a good performance, especially in geriatric GBM patients.
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23
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Zhang Y, Da Q, Cao S, Yan K, Shi Z, Miao Q, Li C, Hu L, Sun S, Wu W, Wu L, Chen F, Wang L, Gao Y, Huang Z, Shao Y, Chen H, Wei Y, Chen F, Han Y, Xie L, Ji Y. HINT1 (Histidine Triad Nucleotide-Binding Protein 1) Attenuates Cardiac Hypertrophy Via Suppressing HOXA5 (Homeobox A5) Expression. Circulation 2021; 144:638-654. [PMID: 34098726 DOI: 10.1161/circulationaha.120.051094] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
BACKGROUND Cardiac hypertrophy is an important prepathology of, and will ultimately lead to, heart failure. However, the mechanisms underlying pathological cardiac hypertrophy remain largely unknown. This study aims to elucidate the effects and mechanisms of HINT1 (histidine triad nucleotide-binding protein 1) in cardiac hypertrophy and heart failure. METHODS HINT1 was downregulated in human hypertrophic heart samples compared with nonhypertrophic samples by mass spectrometry analysis. Hint1 knockout mice were challenged with transverse aortic constriction surgery. Cardiac-specific overexpression of HINT1 mice by intravenous injection of adeno-associated virus 9 (AAV9)-encoding Hint1 under the cTnT (cardiac troponin T) promoter were subjected to transverse aortic construction. Unbiased transcriptional analyses were used to identify the downstream targets of HINT1. AAV9 bearing shRNA against Hoxa5 (homeobox A5) was administrated to investigate whether the effects of HINT1 on cardiac hypertrophy were HOXA5-dependent. RNA sequencing analysis was performed to recapitulate possible changes in transcriptome profile.Coimmunoprecipitation assays and cellular fractionation analyses were conducted to examine the mechanism by which HINT1 regulates the expression of HOXA5. RESULTS The reduction of HINT1 expression was observed in the hearts of hypertrophic patients and pressure overloaded-induced hypertrophic mice, respectively. In Hint1-deficient mice, cardiac hypertrophy deteriorated after transverse aortic construction. Conversely, cardiac-specific overexpression of HINT1 alleviated cardiac hypertrophy and dysfunction. Unbiased profiler polymerase chain reaction array showed HOXA5 is 1 target for HINT1, and the cardioprotective role of HINT1 was abolished by HOXA5 knockdown in vivo. Hoxa5 was identified to affect hypertrophy through the TGF-β (transforming growth factor β) signal pathway. Mechanically, HINT1 inhibited PKCβ1 (protein kinase C β type 1) membrane translocation and phosphorylation via direct interaction, attenuating the MEK/ERK/YY1 (mitogen-activated protein kinase/extracellular signal-regulated kinase kinase/yin yang 1) signal pathway, downregulating HOXA5 expression, and eventually attenuating cardiac hypertrophy. CONCLUSIONS HINT1 protects against cardiac hypertrophy through suppressing HOXA5 expression. These findings indicate that HINT1 may be a potential target for therapeutic interventions in cardiac hypertrophy and heart failure.
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Affiliation(s)
- Yan Zhang
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Key Laboratory of Cardiovascular and Cerebrovascular Medicine (Y.Z., Q.D., S.C., K.Y., Z.S., Q.M., C.L., L.H., S.S., Feng Chen, MD, PhD, Y.G., H.C., L.X., Y.J.)
| | - Qiang Da
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Key Laboratory of Cardiovascular and Cerebrovascular Medicine (Y.Z., Q.D., S.C., K.Y., Z.S., Q.M., C.L., L.H., S.S., Feng Chen, MD, PhD, Y.G., H.C., L.X., Y.J.)
| | - Siyi Cao
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Key Laboratory of Cardiovascular and Cerebrovascular Medicine (Y.Z., Q.D., S.C., K.Y., Z.S., Q.M., C.L., L.H., S.S., Feng Chen, MD, PhD, Y.G., H.C., L.X., Y.J.)
| | - Ke Yan
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Key Laboratory of Cardiovascular and Cerebrovascular Medicine (Y.Z., Q.D., S.C., K.Y., Z.S., Q.M., C.L., L.H., S.S., Feng Chen, MD, PhD, Y.G., H.C., L.X., Y.J.)
| | - Zhiguang Shi
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Key Laboratory of Cardiovascular and Cerebrovascular Medicine (Y.Z., Q.D., S.C., K.Y., Z.S., Q.M., C.L., L.H., S.S., Feng Chen, MD, PhD, Y.G., H.C., L.X., Y.J.)
| | - Qing Miao
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Key Laboratory of Cardiovascular and Cerebrovascular Medicine (Y.Z., Q.D., S.C., K.Y., Z.S., Q.M., C.L., L.H., S.S., Feng Chen, MD, PhD, Y.G., H.C., L.X., Y.J.)
| | - Chen Li
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Key Laboratory of Cardiovascular and Cerebrovascular Medicine (Y.Z., Q.D., S.C., K.Y., Z.S., Q.M., C.L., L.H., S.S., Feng Chen, MD, PhD, Y.G., H.C., L.X., Y.J.)
| | - Lulu Hu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Key Laboratory of Cardiovascular and Cerebrovascular Medicine (Y.Z., Q.D., S.C., K.Y., Z.S., Q.M., C.L., L.H., S.S., Feng Chen, MD, PhD, Y.G., H.C., L.X., Y.J.)
| | - Shixiu Sun
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Key Laboratory of Cardiovascular and Cerebrovascular Medicine (Y.Z., Q.D., S.C., K.Y., Z.S., Q.M., C.L., L.H., S.S., Feng Chen, MD, PhD, Y.G., H.C., L.X., Y.J.)
| | - Wei Wu
- Departments of Bioinformatics (W.W., L.Wu)
| | | | - Feng Chen
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Key Laboratory of Cardiovascular and Cerebrovascular Medicine (Y.Z., Q.D., S.C., K.Y., Z.S., Q.M., C.L., L.H., S.S., Feng Chen, MD, PhD, Y.G., H.C., L.X., Y.J.).,Forensic Medicine (Feng Chen, MD, PhD)
| | | | - Yuanqing Gao
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Key Laboratory of Cardiovascular and Cerebrovascular Medicine (Y.Z., Q.D., S.C., K.Y., Z.S., Q.M., C.L., L.H., S.S., Feng Chen, MD, PhD, Y.G., H.C., L.X., Y.J.)
| | - Zhengrong Huang
- Department of Cardiology, the First Affiliated Hospital of Xiamen University, Xiamen, China (Z.H.)
| | - Yongfeng Shao
- Cardiovascular Surgery (Y.S.), the First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Hongshan Chen
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Key Laboratory of Cardiovascular and Cerebrovascular Medicine (Y.Z., Q.D., S.C., K.Y., Z.S., Q.M., C.L., L.H., S.S., Feng Chen, MD, PhD, Y.G., H.C., L.X., Y.J.)
| | - Yongyue Wei
- Department of Biostatistics, School of Public Health (Y.W., Feng Chen, PhD), Nanjing Medical University
| | - Feng Chen
- Department of Biostatistics, School of Public Health (Y.W., Feng Chen, PhD), Nanjing Medical University
| | - Yi Han
- Departments of Geriatrics (Y.H.)
| | - Liping Xie
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Key Laboratory of Cardiovascular and Cerebrovascular Medicine (Y.Z., Q.D., S.C., K.Y., Z.S., Q.M., C.L., L.H., S.S., Feng Chen, MD, PhD, Y.G., H.C., L.X., Y.J.).,The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School (L.X., Y.J.)
| | - Yong Ji
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Key Laboratory of Cardiovascular and Cerebrovascular Medicine (Y.Z., Q.D., S.C., K.Y., Z.S., Q.M., C.L., L.H., S.S., Feng Chen, MD, PhD, Y.G., H.C., L.X., Y.J.).,State Key Laboratory of Reproductive Medicine (Y.J.)
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24
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Le Boiteux E, Court F, Guichet PO, Vaurs-Barrière C, Vaillant I, Chautard E, Verrelle P, Costa BM, Karayan-Tapon L, Fogli A, Arnaud P. Widespread overexpression from the four DNA hypermethylated HOX clusters in aggressive (IDHwt) glioma is associated with H3K27me3 depletion and alternative promoter usage. Mol Oncol 2021; 15:1995-2010. [PMID: 33720519 PMCID: PMC8334257 DOI: 10.1002/1878-0261.12944] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 02/17/2021] [Accepted: 03/12/2021] [Indexed: 12/14/2022] Open
Abstract
In human, the 39 coding HOX genes and 18 referenced noncoding antisense transcripts are arranged in four genomic clusters named HOXA, B, C, and D. This highly conserved family belongs to the homeobox class of genes that encode transcription factors required for normal development. Therefore, HOX gene deregulation might contribute to the development of many cancer types. Here, we study HOX gene deregulation in adult glioma, a common type of primary brain tumor. We performed extensive molecular analysis of tumor samples, classified according to their isocitrate dehydrogenase (IDH1) gene mutation status, and of glioma stem cells. We found widespread expression of sense and antisense HOX transcripts only in aggressive (IDHwt) glioma samples, although the four HOX clusters displayed DNA hypermethylation. Integrative analysis of expression, DNA methylation, and histone modification signatures along the clusters revealed that HOX gene upregulation relies on canonical and alternative bivalent CpG island promoters that escape hypermethylation. H3K27me3 loss at these promoters emerges as the main cause of widespread HOX gene upregulation in IDHwt glioma cell lines and tumors. Our study provides the first comprehensive description of the epigenetic changes at HOX clusters and their contribution to the transcriptional changes observed in adult glioma. It also identified putative 'master' HOX proteins that might contribute to the tumorigenic potential of glioma stem cells.
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Affiliation(s)
- Elisa Le Boiteux
- CNRS, Inserm, GReD, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Franck Court
- CNRS, Inserm, GReD, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Pierre-Olivier Guichet
- INSERM-U1084, Poitiers, France.,Poitiers University, France.,Department of Cancer Biology, Poitiers Hospital, France
| | | | - Isabelle Vaillant
- CNRS, Inserm, GReD, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Emmanuel Chautard
- Pathology Department, Jean Perrin Center, Clermont-Ferrand, France.,INSERM, U1240 IMoST, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Pierre Verrelle
- CIMB, INSERM U1196 CNRS UMR9187, Curie Institute, Orsay, France.,Radiotherapy Department, Curie Institute, Paris, France.,Université Clermont Auvergne, Clermont-Ferrand, France
| | - Bruno M Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, Braga, Portugal.,ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Lucie Karayan-Tapon
- INSERM-U1084, Poitiers, France.,Poitiers University, France.,Department of Cancer Biology, Poitiers Hospital, France
| | - Anne Fogli
- CNRS, Inserm, GReD, Université Clermont Auvergne, Clermont-Ferrand, France.,Biochemistry and Molecular Biology Department, Clermont-Ferrand Hospital, France
| | - Philippe Arnaud
- CNRS, Inserm, GReD, Université Clermont Auvergne, Clermont-Ferrand, France
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25
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Nuechterlein N, Li B, Feroze A, Holland EC, Shapiro L, Haynor D, Fink J, Cimino PJ. Radiogenomic modeling predicts survival-associated prognostic groups in glioblastoma. Neurooncol Adv 2021; 3:vdab004. [PMID: 33615222 PMCID: PMC7883769 DOI: 10.1093/noajnl/vdab004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Background Combined whole-exome sequencing (WES) and somatic copy number alteration (SCNA) information can separate isocitrate dehydrogenase (IDH)1/2-wildtype glioblastoma into two prognostic molecular subtypes, which cannot be distinguished by epigenetic or clinical features. The potential for radiographic features to discriminate between these molecular subtypes has yet to be established. Methods Radiologic features (n = 35 340) were extracted from 46 multisequence, pre-operative magnetic resonance imaging (MRI) scans of IDH1/2-wildtype glioblastoma patients from The Cancer Imaging Archive (TCIA), all of whom have corresponding WES/SCNA data. We developed a novel feature selection method that leverages the structure of extracted MRI features to mitigate the dimensionality challenge posed by the disparity between a large number of features and the limited patients in our cohort. Six traditional machine learning classifiers were trained to distinguish molecular subtypes using our feature selection method, which was compared to least absolute shrinkage and selection operator (LASSO) feature selection, recursive feature elimination, and variance thresholding. Results We were able to classify glioblastomas into two prognostic subgroups with a cross-validated area under the curve score of 0.80 (±0.03) using ridge logistic regression on the 15-dimensional principle component analysis (PCA) embedding of the features selected by our novel feature selection method. An interrogation of the selected features suggested that features describing contours in the T2 signal abnormality region on the T2-weighted fluid-attenuated inversion recovery (FLAIR) MRI sequence may best distinguish these two groups from one another. Conclusions We successfully trained a machine learning model that allows for relevant targeted feature extraction from standard MRI to accurately predict molecularly-defined risk-stratifying IDH1/2-wildtype glioblastoma patient groups.
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Affiliation(s)
- Nicholas Nuechterlein
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington, USA
| | - Beibin Li
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington, USA
| | - Abdullah Feroze
- Department of Neurological Surgery, University of Washington, Seattle, Washington, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Linda Shapiro
- Paul G. Allen School of Computer Science & Engineering, University of Washington, Seattle, Washington, USA
| | - David Haynor
- Department of Radiology, University of Washington, Seattle, Washington, USA
| | - James Fink
- Department of Radiology, University of Washington, Seattle, Washington, USA
| | - Patrick J Cimino
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA.,Department of Pathology, Division of Neuropathology, University of Washington, Seattle, Washington, USA
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26
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Bacolla A, Sengupta S, Ye Z, Yang C, Mitra J, De-Paula RB, Hegde ML, Ahmed Z, Mort M, Cooper DN, Mitra S, Tainer JA. Heritable pattern of oxidized DNA base repair coincides with pre-targeting of repair complexes to open chromatin. Nucleic Acids Res 2021; 49:221-243. [PMID: 33300026 PMCID: PMC7797072 DOI: 10.1093/nar/gkaa1120] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 10/12/2020] [Accepted: 12/07/2020] [Indexed: 12/16/2022] Open
Abstract
Human genome stability requires efficient repair of oxidized bases, which is initiated via damage recognition and excision by NEIL1 and other base excision repair (BER) pathway DNA glycosylases (DGs). However, the biological mechanisms underlying detection of damaged bases among the million-fold excess of undamaged bases remain enigmatic. Indeed, mutation rates vary greatly within individual genomes, and lesion recognition by purified DGs in the chromatin context is inefficient. Employing super-resolution microscopy and co-immunoprecipitation assays, we find that acetylated NEIL1 (AcNEIL1), but not its non-acetylated form, is predominantly localized in the nucleus in association with epigenetic marks of uncondensed chromatin. Furthermore, chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) revealed non-random AcNEIL1 binding near transcription start sites of weakly transcribed genes and along highly transcribed chromatin domains. Bioinformatic analyses revealed a striking correspondence between AcNEIL1 occupancy along the genome and mutation rates, with AcNEIL1-occupied sites exhibiting fewer mutations compared to AcNEIL1-free domains, both in cancer genomes and in population variation. Intriguingly, from the evolutionarily conserved unstructured domain that targets NEIL1 to open chromatin, its damage surveillance of highly oxidation-susceptible sites to preserve essential gene function and to limit instability and cancer likely originated ∼500 million years ago during the buildup of free atmospheric oxygen.
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Affiliation(s)
- Albino Bacolla
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Shiladitya Sengupta
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Weill Cornell Medical College, Cornell University, New York, NY 10065, USA
| | - Zu Ye
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chunying Yang
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Joy Mitra
- Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Ruth B De-Paula
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Muralidhar L Hegde
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Weill Cornell Medical College, Cornell University, New York, NY 10065, USA.,Department of Neurosurgery, Center for Neuroregeneration, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - Zamal Ahmed
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Matthew Mort
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XN, UK
| | - Sankar Mitra
- Department of Radiation Oncology, Houston Methodist Research Institute, Houston, TX 77030, USA.,Weill Cornell Medical College, Cornell University, New York, NY 10065, USA.,Houston Methodist Cancer Center, Houston Methodist Research Institute, Houston, TX 77030, USA
| | - John A Tainer
- Departments of Cancer Biology and of Molecular and Cellular Oncology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
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Horne EA, Diaz P, Cimino PJ, Jung E, Xu C, Hamel E, Wagenbach M, Kumasaka D, Wageling NB, Azorín DD, Winkler F, Wordeman LG, Holland EC, Stella N. A brain-penetrant microtubule-targeting agent that disrupts hallmarks of glioma tumorigenesis. Neurooncol Adv 2020; 3:vdaa165. [PMID: 33506204 PMCID: PMC7813200 DOI: 10.1093/noajnl/vdaa165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Glioma is sensitive to microtubule-targeting agents (MTAs), but most MTAs do not cross the blood brain barrier (BBB). To address this limitation, we developed the new chemical entity, ST-401, a brain-penetrant MTA. METHODS Synthesis of ST-401. Measures of MT assembly and dynamics. Cell proliferation and viability of patient-derived (PD) glioma in culture. Measure of tumor microtube (TM) parameters using immunofluorescence analysis and machine learning-based workflow. Pharmacokinetics (PK) and experimental toxicity in mice. In vivo antitumor activity in the RCAS/tv-a PDGFB-driven glioma (PDGFB-glioma) mouse model. RESULTS We discovered that ST-401 disrupts microtubule (MT) function through gentle and reverisible reduction in MT assembly that triggers mitotic delay and cell death in interphase. ST-401 inhibits the formation of TMs, MT-rich structures that connect glioma to a network that promotes resistance to DNA damage. PK analysis of ST-401 in mice shows brain penetration reaching antitumor concentrations, and in vivo testing of ST-401 in a xenograft flank tumor mouse model demonstrates significant antitumor activity and no over toxicity in mice. In the PDGFB-glioma mouse model, ST-401 enhances the therapeutic efficacies of temozolomide (TMZ) and radiation therapy (RT). CONCLUSION Our study identifies hallmarks of glioma tumorigenesis that are sensitive to MTAs and reports ST-401 as a promising chemical scaffold to develop brain-penetrant MTAs.
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Affiliation(s)
- Eric A Horne
- Department of Pharmacology, University of Washington, Seattle, Washington, USA,Stella Therapeutics, Inc., Pacific Northwest Research Institute, Seattle, Washington, USA
| | - Philippe Diaz
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana, USA,DermaXon LLC, Missoula, Montana, USA
| | - Patrick J Cimino
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Erik Jung
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Cong Xu
- Department of Pharmacology, University of Washington, Seattle, Washington, USA
| | - Ernest Hamel
- Developmental Therapeutics Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Michael Wagenbach
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA
| | - Debra Kumasaka
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | | | - Daniel D Azorín
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Frank Winkler
- Neurology Clinic and National Center for Tumor Diseases, University Hospital Heidelberg, Heidelberg, Germany
| | - Linda G Wordeman
- Department of Physiology and Biophysics, University of Washington, Seattle, Washington, USA
| | - Eric C Holland
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Nephi Stella
- Department of Pharmacology, University of Washington, Seattle, Washington, USA,Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington, USA,Corresponding Author: Nephi Stella, PhD, Department of Psychiatry and Behavioral Sciences, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195-5280, USA ()
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Yang Y, Zhong F, Huang X, Zhang N, Du J, Long Z, Zheng B, Lin W, Liu W, Ma W. High expression of HOXA5 is associated with poor prognosis in acute myeloid leukemia. Curr Probl Cancer 2020; 45:100673. [PMID: 33223227 DOI: 10.1016/j.currproblcancer.2020.100673] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND HOXA5 is considered as an oncogene in many tumors. This study in- vestigated the HOXA5 expression in Chinese acute myeloid leukemia (AML) patients and evaluated the predictive significance of HOXA5 with a single-center retrospective study. METHODS We investigated the expression pattern and prognostic value of HOXA5 in patients with AML through by using a series of databases and various datasets, including the ONCOMINE, TCGA, and STRING datasets. The bone marrow samples of 53 newly diagnosed AML patients (non-M3 subtype) and 19 benign individuals were collected in our center. HOXA5 mRNA expression levels were detected by real-time qPCR, HOXA5 protein expression levels were detected by Western Blot. Clinical data was obtained from inpatient medical records. RESULTS Two microarrays in Oncomine showed that the expression level of HOXA5 was significantly upregulated in AML. Our data revealed that AML patients had higher HOXA5 mRNA and protein expression levels than the controls (P < 0.001). The blast percentage in bone marrow of HOXA5 high-expression group was higher that of HOXA5 low-expression group (P < 0.05). Higher expression level of HOXA5 revealed a worse OS in AML (P < 0.05). CONCLUSION Our findings suggested that HOXA5 might have the potential ability to act as a diagnostic biomarker and potential therapeutic target for AML.
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Affiliation(s)
- You Yang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Department of Pediatrics, Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Fangfang Zhong
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China; Department of Pediatrics, Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China
| | - Xiaoming Huang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Na Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Jingjing Du
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Ze Long
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Bowen Zheng
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Wanjun Lin
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China
| | - Wenjun Liu
- Department of Pediatrics, Affiliated Hospital of Southwest Medical University, Sichuan Clinical Research Center for Birth Defects, Luzhou, Sichuan, China.
| | - Wenzhe Ma
- State Key Laboratory of Quality Research in Chinese Medicine, Macau University of Science and Technology, Macau, China.
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Gonçalves CS, Le Boiteux E, Arnaud P, Costa BM. HOX gene cluster (de)regulation in brain: from neurodevelopment to malignant glial tumours. Cell Mol Life Sci 2020; 77:3797-3821. [PMID: 32239260 PMCID: PMC11105007 DOI: 10.1007/s00018-020-03508-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 03/10/2020] [Accepted: 03/17/2020] [Indexed: 12/19/2022]
Abstract
HOX genes encode a family of evolutionarily conserved homeodomain transcription factors that are crucial both during development and adult life. In humans, 39 HOX genes are arranged in four clusters (HOXA, B, C, and D) in chromosomes 7, 17, 12, and 2, respectively. During embryonic development, particular epigenetic states accompany their expression along the anterior-posterior body axis. This tightly regulated temporal-spatial expression pattern reflects their relative chromosomal localization, and is critical for normal embryonic brain development when HOX genes are mainly expressed in the hindbrain and mostly absent in the forebrain region. Epigenetic marks, mostly polycomb-associated, are dynamically regulated at HOX loci and regulatory regions to ensure the finely tuned HOX activation and repression, highlighting a crucial epigenetic plasticity necessary for homeostatic development. HOX genes are essentially absent in healthy adult brain, whereas they are detected in malignant brain tumours, namely gliomas, where HOX genes display critical roles by regulating several hallmarks of cancer. Here, we review the major mechanisms involved in HOX genes (de)regulation in the brain, from embryonic to adult stages, in physiological and oncologic conditions. We focus particularly on the emerging causes of HOX gene deregulation in glioma, as well as on their functional and clinical implications.
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Affiliation(s)
- Céline S Gonçalves
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Elisa Le Boiteux
- Université Clermont Auvergne, CNRS, INSERM-iGReD, Clermont-Ferrand, France
| | - Philippe Arnaud
- Université Clermont Auvergne, CNRS, INSERM-iGReD, Clermont-Ferrand, France
| | - Bruno M Costa
- Life and Health Sciences Research Institute (ICVS), School of Medicine, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
- ICVS/3B's - PT Government Associate Laboratory, Braga/Guimarães, Portugal.
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30
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Shi T, Guo D, Xu H, Su G, Chen J, Zhao Z, Shi J, Wedemeyer M, Attenello F, Zhang L, Lu W. HOTAIRM1, an enhancer lncRNA, promotes glioma proliferation by regulating long-range chromatin interactions within HOXA cluster genes. Mol Biol Rep 2020; 47:2723-2733. [PMID: 32180085 DOI: 10.1007/s11033-020-05371-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/04/2020] [Indexed: 01/31/2023]
Abstract
The long noncoding RNA HOTAIRM1 reportedly plays important roles in acute myeloid leukemia, gastric cancer and colorectal cancer. Here, we analyzed potential function of HOTAIRM1 in glioma and asked whether it participates in long-range chromatin interactions. We monitored expression of HOTAIRM1 in glioma tissues and correlated levels with patient survival using the TCGA dataset. HOTAIRM1 was highly expressed in glioma tissue, with high levels associated with shortened patient survival time. We then suppressed HOTAIRM1 activity in the human glioblastoma U251 line using CRISPR-cas9 to knock in a truncating polyA fragment. Reporter analysis of these and control cells confirmed that the HOTAIRM1 locus serves as an active enhancer. We then performed Capture-C analysis to identify target genes of that locus and applied RNA antisense purification to assess chromatin interactions between the HOTAIRM1 locus and HOXA cluster genes. HOTAIRM1 knockdown in glioma cells decreased proliferation and reduced expression of HOXA cluster genes. HOTAIRM1 regulates long-range interactions between the HOTAIRM1 locus and HOXA genes. Our work suggests a new mechanism by which HOTAIRM1 regulates glioma progression by regulating high-order chromatin structure and could suggest novel therapeutic targets to treat an intractable cancer.
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Affiliation(s)
- Tengfei Shi
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Dianhao Guo
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Heming Xu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Guangsong Su
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jun Chen
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Zhongfang Zhao
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Jiandang Shi
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China
| | - Michelle Wedemeyer
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Frank Attenello
- Department of Neurological Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Lei Zhang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
| | - Wange Lu
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, 94 Weijin Road, Tianjin, 300071, China.
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31
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Danielsson A, Barreau K, Kling T, Tisell M, Carén H. Accumulation of DNA methylation alterations in paediatric glioma stem cells following fractionated dose irradiation. Clin Epigenetics 2020; 12:26. [PMID: 32046773 PMCID: PMC7014676 DOI: 10.1186/s13148-020-0817-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 01/27/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Radiation is an important therapeutic tool. However, radiotherapy has the potential to promote co-evolution of genetic and epigenetic changes that can drive tumour heterogeneity, formation of radioresistant cells and tumour relapse. There is a clinical need for a better understanding of DNA methylation alterations that may follow radiotherapy to be able to prevent the development of radiation-resistant cells. METHODS We examined radiation-induced changes in DNA methylation profiles of paediatric glioma stem cells (GSCs) in vitro. Five GSC cultures were irradiated in vitro with repeated doses of 2 or 4 Gy. Radiation was given in 3 or 15 fractions. DNA methylation profiling using Illumina DNA methylation arrays was performed at 14 days post-radiation. The cellular characteristics were studied in parallel. RESULTS Few fractions of radiation did not result in significant accumulation of DNA methylation alterations. However, extended dose fractionations changed DNA methylation profiles and induced thousands of differentially methylated positions, specifically in enhancer regions, sites involved in alternative splicing and in repetitive regions. Radiation induced dose-dependent morphological and proliferative alterations of the cells as a consequence of the radiation exposure. CONCLUSIONS DNA methylation alterations of sites with regulatory functions in proliferation and differentiation were identified, which may reflect cellular response to radiation stress through epigenetic reprogramming and differentiation cues.
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Affiliation(s)
- Anna Danielsson
- Sahlgrenska Cancer Center, Department of Oncology, Institute of Clinical Sciences, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
| | - Kristell Barreau
- Sahlgrenska Cancer Center, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Teresia Kling
- Sahlgrenska Cancer Center, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Magnus Tisell
- Department of Clinical Neuroscience and Rehabilitation, Institute of Neuroscience and Physiology, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Helena Carén
- Sahlgrenska Cancer Center, Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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Yoda RA, Marxen T, Longo L, Ene C, Wirsching HG, Keene CD, Holland EC, Cimino PJ. Mitotic Index Thresholds Do Not Predict Clinical Outcome for IDH-Mutant Astrocytoma. J Neuropathol Exp Neurol 2019; 78:1002-1010. [DOI: 10.1093/jnen/nlz082] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 06/15/2019] [Accepted: 08/07/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Current histological grading recommendations for isocitrate dehydrogenase (IDH)-mutant astrocytoma are imprecise and not reliably predictive of patient outcome, while somatic copy number alterations are emerging as important prognostic biomarkers. One explanation for this relative underperformance of histological grading is that current criteria to distinguish World Health Organization (WHO) grade III anaplastic astrocytomas from lower-grade diffuse astrocytomas (WHO grade II) are vague (“increased mitotic activity”). This qualitative approach ensures diagnostic uncertainty and a broad “gray zone” where both diffuse and anaplastic designations can reasonably be assigned. Thus, we hypothesized that interobserver variability and lack of defined mitotic thresholds for IDH-mutant astrocytomas underlies poor predictive accuracy of current histologic grading approaches. To test this hypothesis, we quantified total mitotic figures and maximum mitotic activity per 10 high-powered fields in an institutional cohort of IDH-mutant astrocytomas. In our cohort, there was no mitotic activity threshold that was reflective of progression-free or overall survival (OS). Furthermore, in a multivariate Cox regression model consisting of mitotic activity, molecular markers, and clinical characteristics, only CDKN2A homozygous deletion was identified as a relevant variant for poor OS. We conclude that lack of defined mitotic figure thresholds may not contribute to underperformance of histological grading for IDH-mutant astrocytomas.
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Affiliation(s)
| | - Troy Marxen
- Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Lauren Longo
- Department of Neurology, University Hospital and University of Zurich, Zurich, Switzerland
| | - Chibawanye Ene
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - C Dirk Keene
- Department of Pathology, Division of Neuropathology
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Evangelou P, Groll M, Oppermann H, Gaunitz F, Eisenlöffel C, Müller W, Eschrich K, Schänzer A, Nestler U. Assessment of ApoC1, LuzP6, C12orf75 and OCC-1 in cystic glioblastoma using MALDI-TOF mass spectrometry, immunohistochemistry and qRT-PCR. Med Mol Morphol 2019; 52:217-225. [PMID: 31006040 PMCID: PMC6885021 DOI: 10.1007/s00795-019-00223-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Accepted: 04/08/2019] [Indexed: 12/24/2022]
Abstract
Mass spectrometric analysis of glioblastoma cyst fluids has disclosed a protein peak with m/z 6424–6433. Among the proteins, potentially generating this peak are ApoC1 and LuzP6. To further elucidate protein expression of glioblastoma cells, we analyzed MALDI–TOF results of cyst fluid, performed immunohistochemistry and mRNA analysis. MALDI–TOF protein extraction from 24 glioblastoma cyst fluids was performed with a weak cation exchange. 50 glioblastoma samples were stained with two custom-made antibodies against LuzP6 and commercial antibodies against ApoC1, C12orf75 and OCC-1 and analyzed. For mRNA detection, 16 tissue samples were stored in RNAlater, extracted using the miRNeasy kit and reversely transcribed. For 12 patients, synopsis of results from all three examinations was possible. MALDI–TOF confirmed the peak at 6433 Da in 75% of samples. Immunohistochemically, LuzP6 was detected in 92% (LuzP61–29) and 96% (LuzP630–58) of samples and ApoC1 in 66%. Mean mRNA levels were highest for ApoC1, followed by LuzP6. No correlation between mRNA expression, immunohistochemical staining and intensity of the MALDI–TOF peaks was found. An unequivocal identification of one protein as the source for the 6433 peak is not possible, but our results point to ApoC1 and LuzP6 as the underlying proteins.
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Affiliation(s)
- Petros Evangelou
- Department of Neurosurgery, University Hospital Leipzig, Liebigstrasse 20, 04103, Leipzig, Germany
| | - Mathias Groll
- Department of Neurosurgery, University Hospital Leipzig, Liebigstrasse 20, 04103, Leipzig, Germany
| | - Henry Oppermann
- Department of Neurosurgery, University Hospital Leipzig, Liebigstrasse 20, 04103, Leipzig, Germany
| | - Frank Gaunitz
- Department of Neurosurgery, University Hospital Leipzig, Liebigstrasse 20, 04103, Leipzig, Germany
| | - Christian Eisenlöffel
- Institute of Neuropathology, University Hospital Leipzig, Liebigstrasse 26, 04103, Leipzig, Germany
| | - Wolf Müller
- Institute of Neuropathology, University Hospital Leipzig, Liebigstrasse 26, 04103, Leipzig, Germany
| | - Klaus Eschrich
- Rudolf Schoenheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, Johannisallee 30, 04103, Leipzig, Germany
| | - Anne Schänzer
- Institute of Neuropathology, Justus Liebig University Giessen, 35392, Giessen, Germany
| | - Ulf Nestler
- Department of Neurosurgery, University Hospital Leipzig, Liebigstrasse 20, 04103, Leipzig, Germany.
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The Genetic Landscape of Human Glioblastoma and Matched Primary Cancer Stem Cells Reveals Intratumour Similarity and Intertumour Heterogeneity. Stem Cells Int 2019; 2019:2617030. [PMID: 30984267 PMCID: PMC6431486 DOI: 10.1155/2019/2617030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/01/2019] [Indexed: 12/19/2022] Open
Abstract
Glioblastoma (GBM) is the most malignant human brain tumour, characterized by rapid progression, invasion, intense angiogenesis, high genomic instability, and resistance to therapies. Despite countless experimental researches for new therapeutic strategies and promising clinical trials, the prognosis remains extremely poor, with a mean survival of less than 14 months. GBM aggressive behaviour is due to a subpopulation of tumourigenic stem-like cells, GBM stem cells (GSCs), which hierarchically drive onset, proliferation, and tumour recurrence. The morbidity and mortality of this disease strongly encourage exploring genetic characteristics of GSCs. Here, using array-CGH platform, we investigated genetic and genomic aberration profiles of GBM parent tumour (n = 10) and their primarily derived GSCs. Statistical analysis was performed by using R software and complex heatmap and corrplot packages. Pearson correlation and K-means algorithm were exploited to compare genetic alterations and to group similar genetic profiles in matched pairs of GBM and derived GSCs. We identified, in both GBM and matched GSCs, recurrent copy number alterations, as chromosome 7 polysomy, chromosome 10 monosomy, and chromosome 9p21deletions, which are typical features of primary GBM, essential for gliomagenesis. These observations suggest a condition of strong genomic instability both in GBM as GSCs. Our findings showed the robust similarity between GBM mass and GSCs (Pearson corr.≥0.65) but also highlighted a marked variability among different patients. Indeed, the heatmap reporting Gain/Loss State for 21022 coding/noncoding genes demonstrated high interpatient divergence. Furthermore, K-means algorithm identified an impairment of pathways related to the development and progression of cancer, such as angiogenesis, as well as pathways related to the immune system regulation, such as T cell activation. Our data confirmed the preservation of the genomic landscape from tumour tissue to GSCs, supporting the relevance of this cellular model to test in vitro new target therapies for GBM.
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Specific V-ATPase expression sub-classifies IDHwt lower-grade gliomas and impacts glioma growth in vivo. EBioMedicine 2019; 41:214-224. [PMID: 30737087 PMCID: PMC6441867 DOI: 10.1016/j.ebiom.2019.01.052] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Revised: 01/24/2019] [Accepted: 01/25/2019] [Indexed: 12/27/2022] Open
Abstract
Background Cancer cells use specific V-ATPase subunits to activate oncogenic pathways. Therefore, we investigated V-ATPase deregulation in aggressive gliomas and associated signaling. Methods V-ATPase genes expression and associated pathways were analyzed in different series of glioma available from public databases, as well as in patients' cohort. Activation of pathways was analyzed at gene and protein expression levels. A genetic model of glioma in Drosophila melanogaster and mice with GBM patients-derived orthotopic xenografts were used as in vivo models of disease. Findings GBM and recurrent gliomas display a specific V-ATPase signature. Such signature resolves the heterogeneous class of IDH-wild type lower-grade gliomas, identifying the patients with worse prognosis independently from clinical and molecular features (p = 0·03, by Cox proportional-hazards model). In vivo, V-ATPase subunits deregulation significantly impacts tumor growth and proliferation. At the molecular level, GBM-like V-ATPase expression correlates with upregulation of Homeobox genes. Interpretation Our data identify a V-ATPase signature that accompanies glioma aggressiveness and suggest new entry points for glioma stratification and follow-up. Fund This work was supported by Fondazione Cariplo (2014–1148 to VV), Fondazione IRCCS Ca' Granda, and Fondazione INGM Grant in Molecular Medicine 2014 (to VV).
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Testa U, Castelli G, Pelosi E. Genetic Abnormalities, Clonal Evolution, and Cancer Stem Cells of Brain Tumors. Med Sci (Basel) 2018; 6:E85. [PMID: 30279357 PMCID: PMC6313628 DOI: 10.3390/medsci6040085] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 09/19/2018] [Accepted: 09/25/2018] [Indexed: 02/06/2023] Open
Abstract
Brain tumors are highly heterogeneous and have been classified by the World Health Organization in various histological and molecular subtypes. Gliomas have been classified as ranging from low-grade astrocytomas and oligodendrogliomas to high-grade astrocytomas or glioblastomas. These tumors are characterized by a peculiar pattern of genetic alterations. Pediatric high-grade gliomas are histologically indistinguishable from adult glioblastomas, but they are considered distinct from adult glioblastomas because they possess a different spectrum of driver mutations (genes encoding histones H3.3 and H3.1). Medulloblastomas, the most frequent pediatric brain tumors, are considered to be of embryonic derivation and are currently subdivided into distinct subgroups depending on histological features and genetic profiling. There is emerging evidence that brain tumors are maintained by a special neural or glial stem cell-like population that self-renews and gives rise to differentiated progeny. In many instances, the prognosis of the majority of brain tumors remains negative and there is hope that the new acquisition of information on the molecular and cellular bases of these tumors will be translated in the development of new, more active treatments.
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Affiliation(s)
- Ugo Testa
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Germana Castelli
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
| | - Elvira Pelosi
- Department of Oncology, Istituto Superiore di Sanità, 00161 Rome, Italy.
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