1
|
Hu W, Li D, Yang Y, Zheng Y, Zeng J, Sai K. TIM-3/CD68 double-high expression in Glioma: Prognostic characteristics and potential therapeutic approaches. Int Immunopharmacol 2024; 139:112665. [PMID: 39002523 DOI: 10.1016/j.intimp.2024.112665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Revised: 06/30/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024]
Abstract
BACKGROUND Immunotherapy has revolutionized the treatment of various types of tumors, but there has been no breakthrough in the treatment of gliomas. The aim of this study is to discover valuable immunotherapy target in glioma, analyze its expression in glioma and the related microenvironment, explore potential immunotherapy strategies, and propose new possibilities for the treatment of gliomas. METHODS Immunohistochemistry (IHC) and multiplex fluorescence immunohistochemistry (mIHC) were used to analyze the expression of common immune markers and checkpoints in 187 glioma patients from Sun Yat-sen University Caner Center (SYSUCC). Bioinformatics analysis was used to examine the expression of TIM-3 in different macrophages using the Chinese Glioma Genome Atlas (CGGA) single-cell sequencing database. The Kaplan-Meier curve was used to predict the prognostic value of samples with high TIM-3 and CD68 expression. The R package was used to analyze the somatic mutation status and the sensitivity of small molecule inhibitors in TIM-3/CD68 double-high expression samples. RESULTS TIM-3 is a relatively highly expressed immune checkpoint in glioma. Unlike other tumors, TIM-3 is mainly expressed on macrophages in the glioma microenvironment. TIM-3/CD68 double-high expression suggests poor survival in glioma and may be a new upgrade marker in both IDH-mutant glioma and IDH-wildtype low-grade glioma (LGG) glioma (P < 0.01). Exploring the combination of TIM-3 inhibitors and p38 MAPK inhibitor may be a potential treatment direction for TIM-3/CD68 double high expression gliomas in the future. CONCLUSIONS The combination of TIM-3 and CD68 holds significant importance as a potential target for both prognosis and therapeutic intervention in glioma.
Collapse
Affiliation(s)
- Wanming Hu
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Guangzhou, PR China; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, PR China
| | - Depei Li
- Department of Neurosurgery, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Guangzhou, PR China; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, PR China
| | - Yuanzhong Yang
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Guangzhou, PR China; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, PR China
| | - Yongqiang Zheng
- State Key Laboratory of Oncology in South China, Guangzhou, PR China; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, PR China
| | - Jing Zeng
- Department of Pathology, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Guangzhou, PR China; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, PR China.
| | - Ke Sai
- Department of Neurosurgery, Sun Yat-sen University Cancer Center, Guangzhou, PR China; State Key Laboratory of Oncology in South China, Guangzhou, PR China; Guangdong Provincial Clinical Research Center for Cancer, Guangzhou, PR China.
| |
Collapse
|
2
|
Leung ML, Abdullaev Z, Santana-Santos L, Skaugen JM, Moore S, Ji J. Microarray-Based DNA Methylation Profiling: Validation Considerations for Clinical Testing. J Mol Diagn 2024; 26:447-455. [PMID: 38378079 PMCID: PMC11238273 DOI: 10.1016/j.jmoldx.2024.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Revised: 02/01/2024] [Accepted: 02/08/2024] [Indexed: 02/22/2024] Open
Abstract
Microarray-based methylation profiling has emerged as a valuable tool for refining diagnoses and revealing novel tumor subtypes, particularly in central nervous system tumors. Despite the increasing adoption of this technique in clinical genomic laboratories, no technical standards have been published in establishing minimum criteria for test validation. A working group with experience and expertise in DNA-based methylation profiling tests on central nervous system tumors collaborated to develop practical discussion points and focus on important considerations for validating this test in clinical laboratory settings. The experience in validating this methodology in a clinical setting is summarized. Specifically, the advantages and challenges associated with utilizing an in-house classifier compared with a third-party classifier are highlighted. Additionally, experiences in demonstrating the assay's sensitivity and specificity, establishing minimum sample criteria, and implementing quality control metrics are described. As methylation profiling for tumor classification expands to other tumor types and continues to evolve for various other applications, the critical considerations described here are expected to serve as a guidance for future efforts in establishing professional guidelines for this assay.
Collapse
Affiliation(s)
- Marco L Leung
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio; Departments of Pathology and Pediatrics, The Ohio State University College of Medicine, Columbus, Ohio.
| | - Zied Abdullaev
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Lucas Santana-Santos
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - John M Skaugen
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - Stephen Moore
- Department of Molecular and Medical Genetics and Knight Diagnostic Laboratory, Oregon Health & Science University, Portland, Oregon
| | - Jianling Ji
- Department of Pathology and Laboratory Medicine, Children's Hospital Los Angeles, Los Angeles, California; Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California
| |
Collapse
|
3
|
Drexler R, Khatri R, Sauvigny T, Mohme M, Maire CL, Ryba A, Zghaibeh Y, Dührsen L, Salviano-Silva A, Lamszus K, Westphal M, Gempt J, Wefers AK, Neumann JE, Bode H, Hausmann F, Huber TB, Bonn S, Jütten K, Delev D, Weber KJ, Harter PN, Onken J, Vajkoczy P, Capper D, Wiestler B, Weller M, Snijder B, Buck A, Weiss T, Göller PC, Sahm F, Menstel JA, Zimmer DN, Keough MB, Ni L, Monje M, Silverbush D, Hovestadt V, Suvà ML, Krishna S, Hervey-Jumper SL, Schüller U, Heiland DH, Hänzelmann S, Ricklefs FL. A prognostic neural epigenetic signature in high-grade glioma. Nat Med 2024; 30:1622-1635. [PMID: 38760585 PMCID: PMC11186787 DOI: 10.1038/s41591-024-02969-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 04/03/2024] [Indexed: 05/19/2024]
Abstract
Neural-tumor interactions drive glioma growth as evidenced in preclinical models, but clinical validation is limited. We present an epigenetically defined neural signature of glioblastoma that independently predicts patients' survival. We use reference signatures of neural cells to deconvolve tumor DNA and classify samples into low- or high-neural tumors. High-neural glioblastomas exhibit hypomethylated CpG sites and upregulation of genes associated with synaptic integration. Single-cell transcriptomic analysis reveals a high abundance of malignant stemcell-like cells in high-neural glioblastoma, primarily of the neural lineage. These cells are further classified as neural-progenitor-cell-like, astrocyte-like and oligodendrocyte-progenitor-like, alongside oligodendrocytes and excitatory neurons. In line with these findings, high-neural glioblastoma cells engender neuron-to-glioma synapse formation in vitro and in vivo and show an unfavorable survival after xenografting. In patients, a high-neural signature is associated with decreased overall and progression-free survival. High-neural tumors also exhibit increased functional connectivity in magnetencephalography and resting-state magnet resonance imaging and can be detected via DNA analytes and brain-derived neurotrophic factor in patients' plasma. The prognostic importance of the neural signature was further validated in patients diagnosed with diffuse midline glioma. Our study presents an epigenetically defined malignant neural signature in high-grade gliomas that is prognostically relevant. High-neural gliomas likely require a maximized surgical resection approach for improved outcomes.
Collapse
Affiliation(s)
- Richard Drexler
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Neurology, Stanford University, Stanford, CA, USA
| | - Robin Khatri
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Sauvigny
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malte Mohme
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cecile L Maire
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alice Ryba
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yahya Zghaibeh
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lasse Dührsen
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Amanda Salviano-Silva
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jens Gempt
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annika K Wefers
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia E Neumann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Molecular Neurobiology Hamburg (ZMNH), University Hospital Hamburg Eppendorf, Hamburg, Germany
| | - Helena Bode
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Fabian Hausmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Jütten
- Department of Neurosurgery, University Hospital Aachen, Aachen, Germany
| | - Daniel Delev
- Department of Neurosurgery, University Hospital Aachen, Aachen, Germany
- Department of Neurosurgery, University Clinic Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Katharina J Weber
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
- University Cancer Center (UCT) Frankfurt, Frankfurt am Main, Germany
| | - Patrick N Harter
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Frankfurt am Main, Germany
- Institute of Neuropathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Julia Onken
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Vajkoczy
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Benedikt Wiestler
- Department of Neuroradiology, Klinikum rechts der Isar, School of Medicine, Technical University Munich, Munich, Germany
| | - Michael Weller
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
- Department of Neurology, University of Zürich, Zurich, Switzerland
| | - Berend Snijder
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Alicia Buck
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
- Department of Neurology, University of Zürich, Zurich, Switzerland
| | - Tobias Weiss
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Zurich, Switzerland
- Department of Neurology, University of Zürich, Zurich, Switzerland
| | - Pauline C Göller
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Felix Sahm
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Department of Neuropathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Joelle Aline Menstel
- Department of Neurosurgery, Medical Center University of Freiburg, Freiburg, Germany
| | - David Niklas Zimmer
- Department of Neurosurgery, Medical Center University of Freiburg, Freiburg, Germany
| | | | - Lijun Ni
- Department of Neurology, Stanford University, Stanford, CA, USA
| | - Michelle Monje
- Department of Neurology, Stanford University, Stanford, CA, USA
| | - Dana Silverbush
- Department of Cancer Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Volker Hovestadt
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mario L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Saritha Krishna
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, Research Institute Children's Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dieter H Heiland
- Department of Neurosurgery, University Clinic Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Neurosurgery, Medical Center University of Freiburg, Freiburg, Germany
- Translational Neurosurgery, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
- Department of Neurological Surgery, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
- German Cancer Consortium (DKTK), Partner Site Freiburg, Freiburg, Germany
| | - Sonja Hänzelmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Kidney Health (HCKH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Franz L Ricklefs
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| |
Collapse
|
4
|
Biskup E, Lopacinska-Jørgensen J, Vestergaard LK, Høgdall E. Validating reference-based algorithms to determine cell-type heterogeneity in ovarian cancer DNA methylation studies. Sci Rep 2024; 14:11048. [PMID: 38745057 PMCID: PMC11094148 DOI: 10.1038/s41598-024-61857-y] [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: 02/16/2024] [Accepted: 05/10/2024] [Indexed: 05/16/2024] Open
Abstract
Information about cell composition in tissue samples is crucial for biomarker discovery and prognosis. Specifically, cancer tissue samples present challenges in deconvolution studies due to mutations and genetic rearrangements. Here, we optimized a robust, DNA methylation-based protocol, to be used for deconvolution of ovarian cancer samples. We compared several state-of-the-art methods (HEpiDISH, MethylCIBERSORT and ARIC) and validated the proposed protocol in an in-silico mixture and in an external dataset containing samples from ovarian cancer patients and controls. The deconvolution protocol we eventually implemented is based on MethylCIBERSORT. Comparing deconvolution methods, we paid close attention to the role of a reference panel. We postulate that a possibly high number of samples (in our case: 247) should be used when building a reference panel to ensure robustness and to compensate for biological and technical variation between samples. Subsequently, we tested the performance of the validated protocol in our own study cohort, consisting of 72 patients with malignant and benign ovarian disease as well as in five external cohorts. In conclusion, we refined and validated a reference-based algorithm to determine cell type composition of ovarian cancer tissue samples to be used in cancer biology studies in larger cohorts.
Collapse
Affiliation(s)
- Edyta Biskup
- Department of Pathology, Copenhagen University Hospital, Herlev, Denmark.
| | | | | | - Estrid Høgdall
- Department of Pathology, Copenhagen University Hospital, Herlev, Denmark
| |
Collapse
|
5
|
Drexler R, Khatri R, Schüller U, Eckhardt A, Ryba A, Sauvigny T, Dührsen L, Mohme M, Ricklefs T, Bode H, Hausmann F, Huber TB, Bonn S, Voß H, Neumann JE, Silverbush D, Hovestadt V, Suvà ML, Lamszus K, Gempt J, Westphal M, Heiland DH, Hänzelmann S, Ricklefs FL. Temporal change of DNA methylation subclasses between matched newly diagnosed and recurrent glioblastoma. Acta Neuropathol 2024; 147:21. [PMID: 38244080 PMCID: PMC10799798 DOI: 10.1007/s00401-023-02677-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 12/08/2023] [Accepted: 12/24/2023] [Indexed: 01/22/2024]
Abstract
The longitudinal transition of phenotypes is pivotal in glioblastoma treatment resistance and DNA methylation emerged as an important tool for classifying glioblastoma phenotypes. We aimed to characterize DNA methylation subclass heterogeneity during progression and assess its clinical impact. Matched tissues from 47 glioblastoma patients were subjected to DNA methylation profiling, including CpG-site alterations, tissue and serum deconvolution, mass spectrometry, and immunoassay. Effects of clinical characteristics on temporal changes and outcomes were studied. Among 47 patients, 8 (17.0%) had non-matching classifications at recurrence. In the remaining 39 cases, 28.2% showed dominant DNA methylation subclass transitions, with 72.7% being a mesenchymal subclass. In general, glioblastomas with a subclass transition showed upregulated metabolic processes. Newly diagnosed glioblastomas with mesenchymal transition displayed increased stem cell-like states and decreased immune components at diagnosis and exhibited elevated immune signatures and cytokine levels in serum. In contrast, tissue of recurrent glioblastomas with mesenchymal transition showed increased immune components but decreased stem cell-like states. Survival analyses revealed comparable outcomes for patients with and without subclass transitions. This study demonstrates a temporal heterogeneity of DNA methylation subclasses in 28.2% of glioblastomas, not impacting patient survival. Changes in cell state composition associated with subclass transition may be crucial for recurrent glioblastoma targeted therapies.
Collapse
Affiliation(s)
- Richard Drexler
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Robin Khatri
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, Research Institute Children's Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Alicia Eckhardt
- Department of Pediatric Hematology and Oncology, Research Institute Children's Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
- Department of Radiation Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alice Ryba
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Thomas Sauvigny
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Lasse Dührsen
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Malte Mohme
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Tammo Ricklefs
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Helena Bode
- Research Institute Children's Cancer Center Hamburg, Hamburg, Germany
| | - Fabian Hausmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hannah Voß
- Section of Mass Spectrometric Proteomics, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia E Neumann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Molecular Neurobiology (ZMNH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Dana Silverbush
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Volker Hovestadt
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mario L Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Jens Gempt
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany
| | - Dieter H Heiland
- Department of Neurosurgery, Medical Center University of Freiburg, Freiburg, Germany
| | - Sonja Hänzelmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Franz L Ricklefs
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Martinistrasse 52, 20246, Hamburg, Germany.
| |
Collapse
|
6
|
Hadad S, Gupta R, Oberheim Bush NA, Taylor JW, Villanueva-Meyer JE, Young JS, Wu J, Ravindranathan A, Zhang Y, Warrier G, McCoy L, Shai A, Pekmezci M, Perry A, Bollen AW, Phillips JJ, Braunstein SE, Raleigh DR, Theodosopoulos P, Aghi MK, Chang EF, Hervey-Jumper SL, Costello JF, de Groot J, Butowski NA, Clarke JL, Chang SM, Berger MS, Molinaro AM, Solomon DA. "De novo replication repair deficient glioblastoma, IDH-wildtype" is a distinct glioblastoma subtype in adults that may benefit from immune checkpoint blockade. Acta Neuropathol 2023; 147:3. [PMID: 38079020 PMCID: PMC10713691 DOI: 10.1007/s00401-023-02654-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/24/2023] [Accepted: 10/24/2023] [Indexed: 12/18/2023]
Abstract
Glioblastoma is a clinically and molecularly heterogeneous disease, and new predictive biomarkers are needed to identify those patients most likely to respond to specific treatments. Through prospective genomic profiling of 459 consecutive primary treatment-naïve IDH-wildtype glioblastomas in adults, we identified a unique subgroup (2%, 9/459) defined by somatic hypermutation and DNA replication repair deficiency due to biallelic inactivation of a canonical mismatch repair gene. The deleterious mutations in mismatch repair genes were often present in the germline in the heterozygous state with somatic inactivation of the remaining allele, consistent with glioblastomas arising due to underlying Lynch syndrome. A subset of tumors had accompanying proofreading domain mutations in the DNA polymerase POLE and resultant "ultrahypermutation". The median age at diagnosis was 50 years (range 27-78), compared with 63 years for the other 450 patients with conventional glioblastoma (p < 0.01). All tumors had histologic features of the giant cell variant of glioblastoma. They lacked EGFR amplification, lacked combined trisomy of chromosome 7 plus monosomy of chromosome 10, and only rarely had TERT promoter mutation or CDKN2A homozygous deletion, which are hallmarks of conventional IDH-wildtype glioblastoma. Instead, they harbored frequent inactivating mutations in TP53, NF1, PTEN, ATRX, and SETD2 and recurrent activating mutations in PDGFRA. DNA methylation profiling revealed they did not align with known reference adult glioblastoma methylation classes, but instead had unique globally hypomethylated epigenomes and mostly classified as "Diffuse pediatric-type high grade glioma, RTK1 subtype, subclass A". Five patients were treated with immune checkpoint blockade, four of whom survived greater than 3 years. The median overall survival was 36.8 months, compared to 15.5 months for the other 450 patients (p < 0.001). We conclude that "De novo replication repair deficient glioblastoma, IDH-wildtype" represents a biologically distinct subtype in the adult population that may benefit from prospective identification and treatment with immune checkpoint blockade.
Collapse
Affiliation(s)
- Sara Hadad
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Rohit Gupta
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Nancy Ann Oberheim Bush
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Jennie W Taylor
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Javier E Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California, San Francisco, San Francisco, CA, USA
| | - Jacob S Young
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jasper Wu
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Ajay Ravindranathan
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Yalan Zhang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Gayathri Warrier
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Lucie McCoy
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Anny Shai
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Melike Pekmezci
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Arie Perry
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Andrew W Bollen
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna J Phillips
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA
| | - Steve E Braunstein
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - David R Raleigh
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Radiation Oncology, University of California, San Francisco, CA, USA
| | - Philip Theodosopoulos
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Manish K Aghi
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Edward F Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Shawn L Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Joseph F Costello
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - John de Groot
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Nicholas A Butowski
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Jennifer L Clarke
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Neurology, University of California, San Francisco, San Francisco, CA, USA
| | - Susan M Chang
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Mitchel S Berger
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Annette M Molinaro
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, USA.
| | - David A Solomon
- Department of Pathology, University of California, San Francisco, San Francisco, CA, USA.
| |
Collapse
|
7
|
Cuomo M, Coretti L, Costabile D, Della Monica R, De Riso G, Buonaiuto M, Trio F, Bravaccio C, Visconti R, Berni Canani R, Chiariotti L, Lembo F. Host fecal DNA specific methylation signatures mark gut dysbiosis and inflammation in children affected by autism spectrum disorder. Sci Rep 2023; 13:18197. [PMID: 37875530 PMCID: PMC10598023 DOI: 10.1038/s41598-023-45132-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 10/16/2023] [Indexed: 10/26/2023] Open
Abstract
The gut-brain axis involves several bidirectional pathway communications including microbiome, bacterial metabolites, neurotransmitters as well as immune system and is perturbed both in brain and in gastrointestinal disorders. Consistently, microbiota-gut-brain axis has been found altered in autism spectrum disorder (ASD). We reasoned that such alterations occurring in ASD may impact both on methylation signatures of human host fecal DNA (HFD) and possibly on the types of human cells shed in the stools from intestinal tract giving origin to HFD. To test this hypothesis, we have performed whole genome methylation analysis of HFD from an age-restricted cohort of young children with ASD (N = 8) and healthy controls (N = 7). In the same cohort we have previously investigated the fecal microbiota composition and here we refined such analysis and searched for eventual associations with data derived from HFD methylome analysis. Our results showed that specific epigenetic signatures in human fecal DNA, especially at genes related to inflammation, associated with the disease. By applying methylation-based deconvolution algorithm, we found that the HFD derived mainly from immune cells and the relative abundance of those differed between patients and controls. Consistently, most of differentially methylated regions fitted with genes involved in inflammatory response. Interestingly, using Horvath epigenetic clock, we found that ASD affected children showed both epigenetic and microbiota age accelerated. We believe that the present unprecedented approach may be useful for the identification of the ASD associated HFD epigenetic signatures and may be potentially extended to other brain disorders and intestinal inflammatory diseases.
Collapse
Affiliation(s)
- Mariella Cuomo
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Via S. Pansini 5, 80131, Naples, Italy
- CEINGE Advanced Biotechnologies "Franco Salvatore", Via G. Salvatore 482, 80145, Naples, Italy
| | - Lorena Coretti
- Department of Pharmacy, University of Naples "Federico II", Via Domenico Montesano 49, 80131, Naples, Italy
| | - Davide Costabile
- CEINGE Advanced Biotechnologies "Franco Salvatore", Via G. Salvatore 482, 80145, Naples, Italy
- SEMM-European School of Molecular Medicine, University of Naples "Federico II", Naples, Italy
| | - Rosa Della Monica
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Via S. Pansini 5, 80131, Naples, Italy
- CEINGE Advanced Biotechnologies "Franco Salvatore", Via G. Salvatore 482, 80145, Naples, Italy
| | - Giulia De Riso
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Via S. Pansini 5, 80131, Naples, Italy
| | - Michela Buonaiuto
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Via S. Pansini 5, 80131, Naples, Italy
- CEINGE Advanced Biotechnologies "Franco Salvatore", Via G. Salvatore 482, 80145, Naples, Italy
| | - Federica Trio
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Via S. Pansini 5, 80131, Naples, Italy
- CEINGE Advanced Biotechnologies "Franco Salvatore", Via G. Salvatore 482, 80145, Naples, Italy
| | - Carmela Bravaccio
- Department of Translational Medical Science - Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Roberta Visconti
- Institute for the Experimental Endocrinology and Oncology "G. Salvatore", Italian National Council of Research, Via S. Pansini 5, 80131, Naples, Italy
| | - Roberto Berni Canani
- Department of Translational Medical Science - Pediatric Section, University of Naples Federico II, Naples, Italy
| | - Lorenzo Chiariotti
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples "Federico II", Via S. Pansini 5, 80131, Naples, Italy.
- CEINGE Advanced Biotechnologies "Franco Salvatore", Via G. Salvatore 482, 80145, Naples, Italy.
- SEMM-European School of Molecular Medicine, University of Naples "Federico II", Naples, Italy.
| | - Francesca Lembo
- Department of Pharmacy, University of Naples "Federico II", Via Domenico Montesano 49, 80131, Naples, Italy.
| |
Collapse
|
8
|
Drexler R, Khatri R, Sauvigny T, Mohme M, Maire CL, Ryba A, Zghaibeh Y, Dührsen L, Salviano-Silva A, Lamszus K, Westphal M, Gempt J, Wefers AK, Neumann J, Bode H, Hausmann F, Huber TB, Bonn S, Jütten K, Delev D, Weber KJ, Harter PN, Onken J, Vajkoczy P, Capper D, Wiestler B, Weller M, Snijder B, Buck A, Weiss T, Keough MB, Ni L, Monje M, Silverbush D, Hovestadt V, Suvà ML, Krishna S, Hervey-Jumper SL, Schüller U, Heiland DH, Hänzelmann S, Ricklefs FL. Epigenetic neural glioblastoma enhances synaptic integration and predicts therapeutic vulnerability. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552017. [PMID: 37609137 PMCID: PMC10441357 DOI: 10.1101/2023.08.04.552017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/24/2023]
Abstract
Neural-tumor interactions drive glioma growth as evidenced in preclinical models, but clinical validation is nascent. We present an epigenetically defined neural signature of glioblastoma that independently affects patients' survival. We use reference signatures of neural cells to deconvolve tumor DNA and classify samples into low- or high-neural tumors. High-neural glioblastomas exhibit hypomethylated CpG sites and upregulation of genes associated with synaptic integration. Single-cell transcriptomic analysis reveals high abundance of stem cell-like malignant cells classified as oligodendrocyte precursor and neural precursor cell-like in high-neural glioblastoma. High-neural glioblastoma cells engender neuron-to-glioma synapse formation in vitro and in vivo and show an unfavorable survival after xenografting. In patients, a high-neural signature associates with decreased survival as well as increased functional connectivity and can be detected via DNA analytes and brain-derived neurotrophic factor in plasma. Our study presents an epigenetically defined malignant neural signature in high-grade gliomas that is prognostically relevant.
Collapse
Affiliation(s)
- Richard Drexler
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Neurology, Stanford University, Stanford, CA, 94305, USA
| | - Robin Khatri
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Sauvigny
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Malte Mohme
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Cecile L. Maire
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Alice Ryba
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Yahya Zghaibeh
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lasse Dührsen
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Amanda Salviano-Silva
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Katrin Lamszus
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Manfred Westphal
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jens Gempt
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Annika K. Wefers
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Mildred Scheel Cancer Career Center HaTriCS4, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Julia Neumann
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, Research Institute Children’s Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
| | - Helena Bode
- Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
| | - Fabian Hausmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Tobias B. Huber
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Bonn
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Kerstin Jütten
- Department of Neurosurgery, University Hospital Aachen, Aachen, Germany
| | - Daniel Delev
- Department of Neurosurgery, University Hospital Aachen, Aachen, Germany
| | - Katharina J. Weber
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Frankfurt am Main, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany and German Cancer Research Center (DKFZ), Heidelberg, Germany
- Frankfurt Cancer Institute (FCI), Frankfurt am Main, Germany
- University Cancer Center (UCT) Frankfurt, Frankfurt am Main, Germany
| | - Patrick N. Harter
- Neurological Institute (Edinger Institute), University Hospital Frankfurt, Frankfurt am Main, Germany
- Institute of Neuropathology, Faculty of Medicine, LMU Munich, Munich, Germany
| | - Julia Onken
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Vajkoczy
- Department of Neurosurgery, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - David Capper
- Department of Neuropathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Charitéplatz 1, 10117 Berlin, Germany
| | - Benedikt Wiestler
- Department of Neuroradiology, Klinikum rechts der Isar, School of Medicine, Technical University Munich, Munich
| | - Michael Weller
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Switzerland. Department of Neurology, University of Zürich, Switzerland
| | - Berend Snijder
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Alicia Buck
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Switzerland. Department of Neurology, University of Zürich, Switzerland
| | - Tobias Weiss
- Department of Neurology, Clinical Neuroscience Center, University Hospital Zurich, Switzerland. Department of Neurology, University of Zürich, Switzerland
| | - Michael B. Keough
- Department of Neurology, Stanford University, Stanford, CA, 94305, USA
| | - Lijun Ni
- Department of Neurology, Stanford University, Stanford, CA, 94305, USA
| | - Michelle Monje
- Department of Neurology, Stanford University, Stanford, CA, 94305, USA
| | | | | | - Mario L. Suvà
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Saritha Krishna
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Shawn L. Hervey-Jumper
- Department of Neurological Surgery, University of California, San Francisco, San Francisco, CA, 94143, USA
| | - Ulrich Schüller
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Department of Pediatric Hematology and Oncology, Research Institute Children’s Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Research Institute Children’s Cancer Center Hamburg, Hamburg, Germany
| | - Dieter H. Heiland
- Department of Neurosurgery, Medical Center University of Freiburg, Freiburg, Germany
| | - Sonja Hänzelmann
- Institute of Medical Systems Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Center for Biomedical AI, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
- Hamburg Center for Translational Immunology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Franz L. Ricklefs
- Department of Neurosurgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| |
Collapse
|
9
|
Neely AM, Yang M, Marconett CN. CLOCK'ing differences in DNA methylation signatures to understand the molecular etiology of lung cancer. Transl Lung Cancer Res 2023; 12:1338-1341. [PMID: 37425400 PMCID: PMC10326774 DOI: 10.21037/tlcr-23-65] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 03/23/2023] [Indexed: 07/11/2023]
Affiliation(s)
- Aaron M. Neely
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Minxiao Yang
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Crystal N. Marconett
- Department of Translational Genomics, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Hastings Center for Pulmonary Research, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Surgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Department of Biochemistry and Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
10
|
Dang H, Khan AB, Gadgil N, Sharma H, Trandafir C, Malbari F, Weiner HL. Behavioral Improvements following Lesion Resection for Pediatric Epilepsy: Pediatric Psychosurgery? Pediatr Neurosurg 2023; 58:80-88. [PMID: 36787706 PMCID: PMC10233708 DOI: 10.1159/000529683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 02/08/2023] [Indexed: 02/16/2023]
Abstract
INTRODUCTION Resection of brain lesions associated with refractory epilepsy to achieve seizure control is well accepted. However, concurrent behavioral effects of these lesions such as changes in mood, personality, and cognition and the effects of surgery on behavior have not been well characterized. We describe 5 such children with epileptogenic lesions and significant behavioral abnormalities which improved after surgery. CASE DESCRIPTIONS Five children (ages 3-14 years) with major behavioral abnormalities and lesional epilepsy were identified and treated at our center. Behavioral problems included academic impairment, impulsivity, self-injurious behavior, and decreased social interaction with diagnoses of ADHD, oppositional defiant disorder, and autism. Pre-operative neuropsychiatric testing was performed in 4/5 patients and revealed low-average cognitive and intellectual abilities for their age, attentional difficulties, and poor memory. Lesions were located in the temporal (2 gangliogliomas, 1 JPA, 1 cavernoma) and parietal (1 DNET) lobes. Gross total resection was achieved in all cases. At mean 1-year follow-up, seizure freedom (Engel 1a in 3 patients, Engel 1c in 2 patients) and significant behavioral improvements (academic performance, attention, socialization, and aggression) were achieved in all. Two patients manifested violence pre-operatively; one had extreme behavior with violence toward teachers and peers despite low seizure burden. Since surgery, his behavior has normalized. CONCLUSION We identified 5 patients with severe behavioral disorders in the setting of lesional epilepsy, all of whom demonstrated improvement after surgery. The degree of behavioral abnormality was disproportionate to epilepsy severity, suggesting a more complicated mechanism by which lesional epilepsy impacts behavior. We propose a novel paradigm in which lesionectomy may offer behavioral benefit even when seizures are not refractory. Thus, behavioral improvement may be an important novel goal for neurosurgical resection in children with epileptic brain lesions.
Collapse
Affiliation(s)
- Huy Dang
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA,
| | - Abdul Basit Khan
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA
| | - Nisha Gadgil
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA
- Division of Pediatric Neurosurgery, Department of Surgery, Texas Children's Hospital, Houston, Texas, USA
| | - Himanshu Sharma
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA
| | - Cristina Trandafir
- Department of Neurology, Baylor College of Medicine, Houston, Texas, USA
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Texas Children's Hospital, Houston, Texas, USA
| | - Fatema Malbari
- Department of Neurology, Baylor College of Medicine, Houston, Texas, USA
- Division of Neurology and Developmental Neuroscience, Department of Pediatrics, Texas Children's Hospital, Houston, Texas, USA
| | - Howard L Weiner
- Department of Neurosurgery, Baylor College of Medicine, Houston, Texas, USA
- Division of Pediatric Neurosurgery, Department of Surgery, Texas Children's Hospital, Houston, Texas, USA
| |
Collapse
|
11
|
Expanded analysis of high-grade astrocytoma with piloid features identifies an epigenetically and clinically distinct subtype associated with neurofibromatosis type 1. Acta Neuropathol 2023; 145:71-82. [PMID: 36271929 PMCID: PMC9844520 DOI: 10.1007/s00401-022-02513-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/16/2022] [Accepted: 10/16/2022] [Indexed: 01/25/2023]
Abstract
High-grade astrocytoma with piloid features (HGAP) is a recently recognized glioma type whose classification is dependent on its global epigenetic signature. HGAP is characterized by alterations in the mitogen-activated protein kinase (MAPK) pathway, often co-occurring with CDKN2A/B homozygous deletion and/or ATRX mutation. Experience with HGAP is limited and to better understand this tumor type, we evaluated an expanded cohort of patients (n = 144) with these tumors, as defined by DNA methylation array testing, with a subset additionally evaluated by next-generation sequencing (NGS). Among evaluable cases, we confirmed the high prevalence CDKN2A/B homozygous deletion, and/or ATRX mutations/loss in this tumor type, along with a subset showing NF1 alterations. Five of 93 (5.4%) cases sequenced harbored TP53 mutations and RNA fusion analysis identified a single tumor containing an NTRK2 gene fusion, neither of which have been previously reported in HGAP. Clustering analysis revealed the presence of three distinct HGAP subtypes (or groups = g) based on whole-genome DNA methylation patterns, which we provisionally designated as gNF1 (n = 18), g1 (n = 72), and g2 (n = 54) (median ages 43.5 years, 47 years, and 32 years, respectively). Subtype gNF1 is notable for enrichment with patients with Neurofibromatosis Type 1 (33.3%, p = 0.0008), confinement to the posterior fossa, hypermethylation in the NF1 enhancer region, a trend towards decreased progression-free survival (p = 0.0579), RNA processing pathway dysregulation, and elevated non-neoplastic glia and neuron cell content (p < 0.0001 and p < 0.0001, respectively). Overall, our expanded cohort broadens the genetic, epigenetic, and clinical phenotype of HGAP and provides evidence for distinct epigenetic subtypes in this tumor type.
Collapse
|
12
|
Estevez-Ordonez D, Gary SE, Atchley TJ, Maleknia PD, George JA, Laskay NMB, Gross EG, Devulapalli RK, Johnston JM. Immunotherapy for Pediatric Brain and Spine Tumors: Current State and Future Directions. Pediatr Neurosurg 2022; 58:313-336. [PMID: 36549282 PMCID: PMC10233708 DOI: 10.1159/000528792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 12/15/2022] [Indexed: 12/24/2022]
Abstract
BACKGROUND Brain tumors are the most common solid tumors and the leading cause of cancer-related deaths in children. Incidence in the USA has been on the rise for the last 2 decades. While therapeutic advances in diagnosis and treatment have improved survival and quality of life in many children, prognosis remains poor and current treatments have significant long-term sequelae. SUMMARY There is a substantial need for the development of new therapeutic approaches, and since the introduction of immunotherapy by immune checkpoint inhibitors, there has been an exponential increase in clinical trials to adopt these and other immunotherapy approaches in children with brain tumors. In this review, we summarize the current immunotherapy landscape for various pediatric brain tumor types including choroid plexus tumors, embryonal tumors (medulloblastoma, AT/RT, PNETs), ependymoma, germ cell tumors, gliomas, glioneuronal and neuronal tumors, and mesenchymal tumors. We discuss the latest clinical trials and noteworthy preclinical studies to treat these pediatric brain tumors using checkpoint inhibitors, cellular therapies (CAR-T, NK, T cell), oncolytic virotherapy, radioimmunotherapy, tumor vaccines, immunomodulators, and other targeted therapies. KEY MESSAGES The current landscape for immunotherapy in pediatric brain tumors is still emerging, but results in certain tumors have been promising. In the age of targeted therapy, genetic tumor profiling, and many ongoing clinical trials, immunotherapy will likely become an increasingly effective tool in the neuro-oncologist armamentarium.
Collapse
Affiliation(s)
- Dagoberto Estevez-Ordonez
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, USA,
- Division of Pediatric Neurosurgery, Children's of Alabama, Birmingham, Alabama, USA,
| | - Sam E Gary
- Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Travis J Atchley
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Division of Pediatric Neurosurgery, Children's of Alabama, Birmingham, Alabama, USA
| | - Pedram D Maleknia
- Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Jordan A George
- Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Nicholas M B Laskay
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Division of Pediatric Neurosurgery, Children's of Alabama, Birmingham, Alabama, USA
| | - Evan G Gross
- Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Rishi K Devulapalli
- Heersink School of Medicine, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - James M Johnston
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, Alabama, USA
- Division of Pediatric Neurosurgery, Children's of Alabama, Birmingham, Alabama, USA
| |
Collapse
|
13
|
Tiwari A, Trivedi R, Lin SY. Tumor microenvironment: barrier or opportunity towards effective cancer therapy. J Biomed Sci 2022; 29:83. [PMID: 36253762 PMCID: PMC9575280 DOI: 10.1186/s12929-022-00866-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/01/2022] [Indexed: 12/24/2022] Open
Abstract
Tumor microenvironment (TME) is a specialized ecosystem of host components, designed by tumor cells for successful development and metastasis of tumor. With the advent of 3D culture and advanced bioinformatic methodologies, it is now possible to study TME’s individual components and their interplay at higher resolution. Deeper understanding of the immune cell’s diversity, stromal constituents, repertoire profiling, neoantigen prediction of TMEs has provided the opportunity to explore the spatial and temporal regulation of immune therapeutic interventions. The variation of TME composition among patients plays an important role in determining responders and non-responders towards cancer immunotherapy. Therefore, there could be a possibility of reprogramming of TME components to overcome the widely prevailing issue of immunotherapeutic resistance. The focus of the present review is to understand the complexity of TME and comprehending future perspective of its components as potential therapeutic targets. The later part of the review describes the sophisticated 3D models emerging as valuable means to study TME components and an extensive account of advanced bioinformatic tools to profile TME components and predict neoantigens. Overall, this review provides a comprehensive account of the current knowledge available to target TME.
Collapse
Affiliation(s)
- Aadhya Tiwari
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Rakesh Trivedi
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Shiaw-Yih Lin
- Department of Systems Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| |
Collapse
|