1
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Xie H, Jiang Y, Xiang Y, Wu B, Zhao J, Huang R, Wang M, Wang Y, Liu J, Wu D, Tian D, Bian E. Super-enhancer-driven LIF promotes the mesenchymal transition in glioblastoma by activating ITGB2 signaling feedback in microglia. Neuro Oncol 2024; 26:1438-1452. [PMID: 38554116 PMCID: PMC11300025 DOI: 10.1093/neuonc/noae065] [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: 09/12/2023] [Indexed: 04/01/2024] Open
Abstract
BACKGROUND The mesenchymal (MES) subtype of glioblastoma (GBM) is believed to be influenced by both cancer cell-intrinsic alterations and extrinsic cellular interactions, yet the underlying mechanisms remain unexplored. METHODS Identification of microglial heterogeneity by bioinformatics analysis. Transwell migration, invasion assays, and tumor models were used to determine gene function and the role of small molecule inhibitors. RNA sequencing, chromatin immunoprecipitation, and dual-luciferase reporter assays were performed to explore the underlying regulatory mechanisms. RESULTS We identified the inflammatory microglial subtype of tumor-associated microglia (TAM) and found that its specific gene integrin beta 2 (ITGB2) was highly expressed in TAM of MES GBM tissues. Mechanistically, the activation of ITGB2 in microglia promoted the interaction between the SH2 domain of STAT3 and the cytoplasmic domain of ITGB2, thereby stimulating the JAK1/STAT3/IL-6 signaling feedback to promote the MES transition of GBM cells. Additionally, microglia communicated with GBM cells through the interaction between the receptor ITGB2 on microglia and the ligand ICAM-1 on GBM cells, while an increased secretion of ICAM-1 was induced by the proinflammatory cytokine leukemia inhibitory factor (LIF). Further studies demonstrated that inhibition of cyclin-dependent kinase 7 substantially reduced the recruitment of SNW1 to the super-enhancer of LIF, resulting in transcriptional inhibition of LIF. We identified notoginsenoside R1 as a novel LIF inhibitor that exhibited synergistic effects in combination with temozolomide. CONCLUSIONS Our research reveals that the epigenetic-mediated interaction of GBM cells with TAM drives the MES transition of GBM and provides a novel therapeutic avenue for patients with MES GBM.
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Affiliation(s)
- Han Xie
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Hefei, China
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yanyi Jiang
- Institute of Health and Medical Technology, Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei, China
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China
| | - Yufei Xiang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Hefei, China
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Baoming Wu
- School of pharmacy, Anhui Medical University, Hefei, China
| | - Jiajia Zhao
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Hefei, China
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Ruixiang Huang
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Hefei, China
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Mengting Wang
- School of pharmacy, Anhui Medical University, Hefei, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Hefei, China
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Yunlong Wang
- School of pharmacy, Anhui Medical University, Hefei, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Hefei, China
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Jun Liu
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Hefei, China
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Dejun Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Dasheng Tian
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Hefei, China
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Erbao Bian
- School of pharmacy, Anhui Medical University, Hefei, China
- Institute of Orthopaedics, Research Center for Translational Medicine, The Second Hospital of Anhui Medical University, Hefei, China
- Department of Orthopaedics, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
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2
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Li J, Zhang Y, Liang C, Yan X, Hui X, Liu Q. Advancing precision medicine in gliomas through single-cell sequencing: unveiling the complex tumor microenvironment. Front Cell Dev Biol 2024; 12:1396836. [PMID: 39156969 PMCID: PMC11327033 DOI: 10.3389/fcell.2024.1396836] [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: 03/06/2024] [Accepted: 07/22/2024] [Indexed: 08/20/2024] Open
Abstract
Glioblastoma (GBM) displays an infiltrative growth characteristic that recruits neighboring normal cells to facilitate tumor growth, maintenance, and invasion into the brain. While the blood-brain barrier serves as a critical natural defense mechanism for the central nervous system, GBM disrupts this barrier, resulting in the infiltration of macrophages from the peripheral bone marrow and the activation of resident microglia. Recent advancements in single-cell transcriptomics and spatial transcriptomics have refined the categorization of cells within the tumor microenvironment for precise identification. The intricate interactions and influences on cell growth within the tumor microenvironment under multi-omics conditions are succinctly outlined. The factors and mechanisms involving microglia, macrophages, endothelial cells, and T cells that impact the growth of GBM are individually examined. The collaborative mechanisms of tumor cell-immune cell interactions within the tumor microenvironment synergistically promote the growth, infiltration, and metastasis of gliomas, while also influencing the immune status and therapeutic response of the tumor microenvironment. As immunotherapy continues to progress, targeting the cells within the inter-tumor microenvironment emerges as a promising novel therapeutic approach for GBM. By comprehensively understanding and intervening in the intricate cellular interactions within the tumor microenvironment, novel therapeutic modalities may be developed to enhance treatment outcomes for patients with GBM.
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Affiliation(s)
- Jinwei Li
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
- Department of Neurosurgery, Liuzhou Workers Hospital, Liuzhou, Guangxi, China
| | - Yang Zhang
- Graduate School of Medicine, Kunming Medical University, Kunming, Yunnan, China
| | - Cong Liang
- Department of Pharmacy, Liuzhou Workers Hospital, Liuzhou, Guangxi, China
| | - Xianlei Yan
- Department of Neurosurgery, Liuzhou Workers Hospital, Liuzhou, Guangxi, China
| | - Xuhui Hui
- Department of Neurosurgery, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Quan Liu
- Department of Neurosurgery, Liuzhou Workers Hospital, Liuzhou, Guangxi, China
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3
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Chagas PS, Chagas HIS, Naeini SE, Bhandari B, Gouron J, Malta TM, Salles ÉL, Wang LP, Yu JC, Baban B. Network-Based Transcriptome Analysis Reveals FAM3C as a Novel Potential Biomarker for Glioblastoma. J Cell Biochem 2024; 125:e30612. [PMID: 38923575 DOI: 10.1002/jcb.30612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024]
Abstract
Glioblastoma (GBM) is the most common form of malignant primary brain tumor with a high mortality rate. The aim of the present study was to investigate the clinical significance of Family with Sequence Similarity 3, Member C, FAM3C, in GBM using bioinformatic-integrated analysis. First, we performed the transcriptomic integration analysis to assess the expression profile of FAM3C in GBM using several data sets (RNA-sequencing and scRNA-sequencing), which were obtained from TCGA and GEO databases. By using the STRING platform, we investigated FAM3C-coregulated genes to construct the protein-protein interaction network. Next, Metascape, Enrichr, and CIBERSORT databases were used. We found FAM3C high expression in GBM with poor survival rates. Further, we observed, via FAM3C coexpression network analysis, that FAM3C plays key roles in several hallmarks of cancer. Surprisingly, we also highlighted five FAM3C‑coregulated genes overexpressed in GBM. Specifically, we demonstrated the association between the high expression of FAM3C and the abundance of the different immune cells, which may markedly worsen GBM prognosis. For the first time, our findings suggest that FAM3C not only can be a new emerging biomarker with promising therapeutic values to GBM patients but also gave a new insight into a potential resource for future GBM studies.
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Affiliation(s)
- Pablo Shimaoka Chagas
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, Georgia, USA
- DCG Center for Excellence in Research, Scholarship and Innovation (CERSI) Augusta University, Augusta, Georgia, USA
| | | | - Sahar Emami Naeini
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Bidhan Bhandari
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Jules Gouron
- DCG Center for Excellence in Research, Scholarship and Innovation (CERSI) Augusta University, Augusta, Georgia, USA
| | - Tathiane M Malta
- Department of Clinical Analyses, Toxicology and Food Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, Brazil
| | - Évila Lopes Salles
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Lei P Wang
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, Georgia, USA
- DCG Center for Excellence in Research, Scholarship and Innovation (CERSI) Augusta University, Augusta, Georgia, USA
- Georgia Institute of Cannabis Research, Medicinal Cannabis of Georgia LLC, Augusta, Georgia, USA
| | - Jack C Yu
- Department of Surgery, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
| | - Babak Baban
- Department of Oral Biology and Diagnostic Sciences, Dental College of Georgia, Augusta University, Augusta, Georgia, USA
- DCG Center for Excellence in Research, Scholarship and Innovation (CERSI) Augusta University, Augusta, Georgia, USA
- Georgia Institute of Cannabis Research, Medicinal Cannabis of Georgia LLC, Augusta, Georgia, USA
- Department of Neurology, Medical College of Georgia, Augusta University, Augusta, Georgia, USA
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4
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Yalamandala B, Chen YJ, Lin YH, Huynh TMH, Chiang WH, Chou TC, Liu HW, Huang CC, Lu YJ, Chiang CS, Chu LA, Hu SH. A Self-Cascade Penetrating Brain Tumor Immunotherapy Mediated by Near-Infrared II Cell Membrane-Disrupting Nanoflakes via Detained Dendritic Cells. ACS NANO 2024; 18:18712-18728. [PMID: 38952208 PMCID: PMC11256899 DOI: 10.1021/acsnano.4c06183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 06/24/2024] [Accepted: 06/25/2024] [Indexed: 07/03/2024]
Abstract
Immunotherapy can potentially suppress the highly aggressive glioblastoma (GBM) by promoting T lymphocyte infiltration. Nevertheless, the immune privilege phenomenon, coupled with the generally low immunogenicity of vaccines, frequently hampers the presence of lymphocytes within brain tumors, particularly in brain tumors. In this study, the membrane-disrupted polymer-wrapped CuS nanoflakes that can penetrate delivery to deep brain tumors via releasing the cell-cell interactions, facilitating the near-infrared II (NIR II) photothermal therapy, and detaining dendritic cells for a self-cascading immunotherapy are developed. By convection-enhanced delivery, membrane-disrupted amphiphilic polymer micelles (poly(methoxypoly(ethylene glycol)-benzoic imine-octadecane, mPEG-b-C18) with CuS nanoflakes enhances tumor permeability and resides in deep brain tumors. Under low-power NIR II irradiation (0.8 W/cm2), the intense heat generated by well-distributed CuS nanoflakes actuates the thermolytic efficacy, facilitating cell apoptosis and the subsequent antigen release. Then, the positively charged polymer after hydrolysis of the benzoic-imine bond serves as an antigen depot, detaining autologous tumor-associated antigens and presenting them to dendritic cells, ensuring sustained immune stimulation. This self-cascading penetrative immunotherapy amplifies the immune response to postoperative brain tumors but also enhances survival outcomes through effective brain immunotherapy.
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Affiliation(s)
- Bhanu
Nirosha Yalamandala
- Department
of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Yu-Jen Chen
- Department
of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Ya-Hui Lin
- Department
of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
- Brain
Research Center, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Thi My Hue Huynh
- Department
of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Wen-Hsuan Chiang
- Department
of Chemical Engineering, National Chung
Hsing University, Taichung 402, Taiwan
| | - Tsu-Chin Chou
- Institute
of Analytical and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Heng-Wei Liu
- Department
of Neurosurgery, Shuang Ho Hospital, Taipei
Medical University, New Taipei
City 23561, Taiwan
- Taipei Neuroscience
Institute, Taipei Medical University, Taipei 11031, Taiwan
- Department
of Surgery, School of Medicine, College of Medicine, Taipei Medical University, Taipei 11031, Taiwan
| | - Chieh-Cheng Huang
- Institute
of Biomedical Engineering, National Tsing
Hua University, Hsinchu 300044, Taiwan
| | - Yu-Jen Lu
- Department
of Neurosurgery, Chang Gung Memorial Hospital, College of Medicine, Chang Gung University, Taoyuan 33305, Taiwan
- College
of Medicine, Chang Gung University, Kwei-San, Taoyuan 33302, Taiwan
| | - Chi-Shiun Chiang
- Department
of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Li-An Chu
- Department
of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
- Brain
Research Center, National Tsing Hua University, Hsinchu 300044, Taiwan
| | - Shang-Hsiu Hu
- Department
of Biomedical Engineering and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
- Institute
of Analytical and Environmental Sciences, National Tsing Hua University, Hsinchu 300044, Taiwan
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5
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Salvalaggio A, Pini L, Bertoldo A, Corbetta M. Glioblastoma and brain connectivity: the need for a paradigm shift. Lancet Neurol 2024; 23:740-748. [PMID: 38876751 DOI: 10.1016/s1474-4422(24)00160-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 02/29/2024] [Accepted: 04/03/2024] [Indexed: 06/16/2024]
Abstract
Despite substantial advances in cancer treatment, for patients with glioblastoma prognosis remains bleak. The emerging field of cancer neuroscience reveals intricate functional interplays between glioblastoma and the cellular architecture of the brain, encompassing neurons, glia, and vessels. New findings underscore the role of structural and functional connections within hierarchical networks, known as the connectome. These connections contribute to the location, spread, and recurrence of a glioblastoma, and a patient's overall survival, revealing a complex interplay between the tumour and the CNS. This mounting evidence prompts a paradigm shift, challenging the perception of glioblastomas as mere foreign bodies within the brain. Instead, these tumours are intricately woven into the structural and functional fabric of the brain. This radical change in thinking holds profound implications for the understanding and treatment of glioblastomas, which could unveil new prognostic factors and surgical strategies and optimise radiotherapy. Additionally, a connectivity approach suggests that non-invasive brain stimulation could disrupt pathological neuron-glioma interactions within specific networks.
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Affiliation(s)
- Alessandro Salvalaggio
- Clinica Neurologica, Azienda Ospedale Università Padova, Padova, Italy; Department of Neuroscience, University of Padova, Padova, Italy; Padova Neuroscience Center, University of Padova, Padova, Italy
| | - Lorenzo Pini
- Department of Neuroscience, University of Padova, Padova, Italy
| | - Alessandra Bertoldo
- Padova Neuroscience Center, University of Padova, Padova, Italy; Department of Information Engineering, University of Padova, Padova, Italy
| | - Maurizio Corbetta
- Clinica Neurologica, Azienda Ospedale Università Padova, Padova, Italy; Department of Neuroscience, University of Padova, Padova, Italy; Padova Neuroscience Center, University of Padova, Padova, Italy; Veneto Institute of Molecular Medicine, Fondazione Biomedica, Padova, Italy.
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6
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Read RD, Tapp ZM, Rajappa P, Hambardzumyan D. Glioblastoma microenvironment-from biology to therapy. Genes Dev 2024; 38:360-379. [PMID: 38811170 PMCID: PMC11216181 DOI: 10.1101/gad.351427.123] [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] [Indexed: 05/31/2024]
Abstract
Glioblastoma (GBM) is the most aggressive primary brain cancer. These tumors exhibit high intertumoral and intratumoral heterogeneity in neoplastic and nonneoplastic compartments, low lymphocyte infiltration, and high abundance of myeloid subsets that together create a highly protumorigenic immunosuppressive microenvironment. Moreover, heterogeneous GBM cells infiltrate adjacent brain tissue, remodeling the neural microenvironment to foster tumor electrochemical coupling with neurons and metabolic coupling with nonneoplastic astrocytes, thereby driving growth. Here, we review heterogeneity in the GBM microenvironment and its role in low-to-high-grade glioma transition, concluding with a discussion of the challenges of therapeutically targeting the tumor microenvironment and outlining future research opportunities.
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Affiliation(s)
- Renee D Read
- Department of Pharmacology and Chemical Biology, Emory University School of Medicine, Atlanta, Georgia 30322, USA;
- Department of Hematology and Medical Oncology, Emory University School of Medicine, Atlanta, Georgia 30322, USA
- Winship Cancer Institute, Emory University School of Medicine, Atlanta, Georgia 30322, USA
| | - Zoe M Tapp
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA
| | - Prajwal Rajappa
- The Steve and Cindy Rasmussen Institute for Genomic Medicine, Nationwide Children's Hospital, Columbus, Ohio 43205, USA;
- Department of Pediatrics, The Ohio State University Wexner Medical Center, Columbus, Ohio 43215, USA
- Department of Neurological Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio 43215, USA
| | - Dolores Hambardzumyan
- Department of Oncological Sciences, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA;
- Department of Neurosurgery, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
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7
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Steiner D, Sultan L, Sullivan T, Liu H, Zhang S, LeClerc A, Alekseyev YO, Liu G, Mazzilli SA, Zhang J, Rieger-Christ K, Burks EJ, Beane J, Lenburg ME. Identification of a gene expression signature of vascular invasion and recurrence in stage I lung adenocarcinoma via bulk and spatial transcriptomics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.07.597993. [PMID: 38915565 PMCID: PMC11195124 DOI: 10.1101/2024.06.07.597993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Microscopic vascular invasion (VI) is predictive of recurrence and benefit from lobectomy in stage I lung adenocarcinoma (LUAD) but is difficult to assess in resection specimens and cannot be accurately predicted prior to surgery. Thus, new biomarkers are needed to identify this aggressive subset of stage I LUAD tumors. To assess molecular and microenvironment features associated with angioinvasive LUAD we profiled 162 resected stage I tumors with and without VI by RNA-seq and explored spatial patterns of gene expression in a subset of 15 samples by high-resolution spatial transcriptomics (stRNA-seq). Despite the small size of invaded blood vessels, we identified a gene expression signature of VI from the bulk RNA-seq discovery cohort (n=103) and found that it was associated with VI foci, desmoplastic stroma, and high-grade patterns in our stRNA-seq data. We observed a stronger association with high-grade patterns from VI+ compared with VI- tumors. Using the discovery cohort, we developed a transcriptomic predictor of VI, that in an independent validation cohort (n=60) was associated with VI (AUROC=0.86; p=5.42×10-6) and predictive of recurrence-free survival (HR=1.98; p=0.024), even in VI- LUAD (HR=2.76; p=0.003). To determine our VI predictor's robustness to intra-tumor heterogeneity we used RNA-seq data from multi-region sampling of stage I LUAD cases in TRACERx, where the predictor scores showed high correlation (R=0.87, p<2.2×10-16) between two randomly sampled regions of the same tumor. Our study suggests that VI-associated gene expression changes are detectable beyond the site of intravasation and can be used to predict the presence of VI. This may enable the prediction of angioinvasive LUAD from biopsy specimens, allowing for more tailored medical and surgical management of stage I LUAD.
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Affiliation(s)
- Dylan Steiner
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Lila Sultan
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Travis Sullivan
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, MA, USA
| | - Hanqiao Liu
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Sherry Zhang
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Ashley LeClerc
- Boston University Microarray and Sequencing Resource Core Facility, Boston, MA, USA
| | - Yuriy O Alekseyev
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Gang Liu
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Sarah A Mazzilli
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Jiarui Zhang
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Kimberly Rieger-Christ
- Department of Translational Research, Lahey Hospital and Medical Center, Burlington, MA, USA
| | - Eric J Burks
- Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Jennifer Beane
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
| | - Marc E Lenburg
- Department of Medicine, Section of Computational Biomedicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA, Department of Pathology and Laboratory Medicine, Boston University Chobanian and Avedisian School of Medicine, Boston, MA, USA
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8
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Jiang MQ, Yu SP, Estaba T, Choi E, Berglund K, Gu X, Wei L. Reprogramming Glioblastoma Cells into Non-Cancerous Neuronal Cells as a Novel Anti-Cancer Strategy. Cells 2024; 13:897. [PMID: 38891029 PMCID: PMC11171681 DOI: 10.3390/cells13110897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 05/11/2024] [Accepted: 05/21/2024] [Indexed: 06/20/2024] Open
Abstract
Glioblastoma Multiforme (GBM) is an aggressive brain tumor with a high mortality rate. Direct reprogramming of glial cells to different cell lineages, such as induced neural stem cells (iNSCs) and induced neurons (iNeurons), provides genetic tools to manipulate a cell's fate as a potential therapy for neurological diseases. NeuroD1 (ND1) is a master transcriptional factor for neurogenesis and it promotes neuronal differentiation. In the present study, we tested the hypothesis that the expression of ND1 in GBM cells can force them to differentiate toward post-mitotic neurons and halt GBM tumor progression. In cultured human GBM cell lines, including LN229, U87, and U373 as temozolomide (TMZ)-sensitive and T98G as TMZ-resistant cells, the neuronal lineage conversion was induced by an adeno-associated virus (AAV) package carrying ND1. Twenty-one days after AAV-ND1 transduction, ND1-expressing cells displayed neuronal markers MAP2, TUJ1, and NeuN. The ND1-induced transdifferentiation was regulated by Wnt signaling and markedly enhanced under a hypoxic condition (2% O2 vs. 21% O2). ND1-expressing GBM cultures had fewer BrdU-positive proliferating cells compared to vector control cultures. Increased cell death was visualized by TUNEL staining, and reduced migrative activity was demonstrated in the wound-healing test after ND1 reprogramming in both TMZ-sensitive and -resistant GBM cells. In a striking contrast to cancer cells, converted cells expressed the anti-tumor gene p53. In an orthotopical GBM mouse model, AAV-ND1-reprogrammed U373 cells were transplanted into the fornix of the cyclosporine-immunocompromised C57BL/6 mouse brain. Compared to control GBM cell-formed tumors, cells from ND1-reprogrammed cultures formed smaller tumors and expressed neuronal markers such as TUJ1 in the brain. Thus, reprogramming using a single-factor ND1 overcame drug resistance, converting malignant cells of heterogeneous GBM cells to normal neuron-like cells in vitro and in vivo. These novel observations warrant further research using patient-derived GBM cells and patient-derived xenograft (PDX) models as a potentially effective treatment for a deadly brain cancer and likely other astrocytoma tumors.
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Affiliation(s)
- Michael Q. Jiang
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA 30033, USA; (M.Q.J.); (T.E.); (E.C.); (X.G.)
- Center for Visual and Neurocognitive Rehabilitation, Atlanta Veterans Affairs Medical Center, Decatur, GA 30033, USA
| | - Shan Ping Yu
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA 30033, USA; (M.Q.J.); (T.E.); (E.C.); (X.G.)
- Center for Visual and Neurocognitive Rehabilitation, Atlanta Veterans Affairs Medical Center, Decatur, GA 30033, USA
- Department of Hematology and Oncology, Emory University School of Medicine, Atlanta, GA 30033, USA
| | - Takira Estaba
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA 30033, USA; (M.Q.J.); (T.E.); (E.C.); (X.G.)
| | - Emily Choi
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA 30033, USA; (M.Q.J.); (T.E.); (E.C.); (X.G.)
| | - Ken Berglund
- Department of Neurosurgery, Emory University School of Medicine, Atlanta, GA 30322, USA;
| | - Xiaohuan Gu
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA 30033, USA; (M.Q.J.); (T.E.); (E.C.); (X.G.)
- Center for Visual and Neurocognitive Rehabilitation, Atlanta Veterans Affairs Medical Center, Decatur, GA 30033, USA
| | - Ling Wei
- Department of Anesthesiology, Emory University School of Medicine, Atlanta, GA 30033, USA; (M.Q.J.); (T.E.); (E.C.); (X.G.)
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9
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Bumbaca B, Birtwistle MR, Gallo JM. Network Analyses of Brain Tumor Patients' Multiomic Data Reveals Pharmacological Opportunities to Alter Cell State Transitions. RESEARCH SQUARE 2024:rs.3.rs-4391296. [PMID: 38826227 PMCID: PMC11142360 DOI: 10.21203/rs.3.rs-4391296/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
Glioblastoma Multiforme (GBM) remains a particularly difficult cancer to treat, and survival outcomes remain poor. In addition to the lack of dedicated drug discovery programs for GBM, extensive intratumor heterogeneity and epigenetic plasticity related to cell-state transitions are major roadblocks to successful drug therapy in GBM. To study these phenomenon, publicly available snRNAseq and bulk RNAseq data from patient samples were used to categorize cells from patients into four cell states (i.e. phenotypes), namely: (i) neural progenitor-like (NPC-like), (ii) oligodendrocyte progenitor-like (OPC-like), (iii) astrocyte- like (AC-like), and (iv) mesenchymal-like (MES-like). Patients were subsequently grouped into subpopulations based on which cell-state was the most dominant in their respective tumor. By incorporating phosphoproteomic measurements from the same patients, a protein-protein interaction network (PPIN) was constructed for each cell state. These four-cell state PPINs were pooled to form a single Boolean network that was used for in silico protein knockout simulations to investigate mechanisms that either promote or prevent cell state transitions. Simulation results were input into a boosted tree machine learning model which predicted the cell states or phenotypes of GBM patients from an independent public data source, the Glioma Longitudinal Analysis (GLASS) Consortium. Combining the simulation results and the machine learning predictions, we generated hypotheses for clinically relevant causal mechanisms of cell state transitions. For example, the transcription factor TFAP2A can be seen to promote a transition from the NPC-like to the MES-like state. Such protein nodes and the associated signaling pathways provide potential drug targets that can be further tested in vitro and support cell state-directed (CSD) therapy.
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Affiliation(s)
- Brandon Bumbaca
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo NY, USA
| | - Marc R Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson SC, USA
- Department of Bioengineering, Clemson University, Clemson SC, USA
| | - James M Gallo
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo NY, USA
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10
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Williams TL, Nwokoye P, Kuc RE, Smith K, Paterson AL, Allinson K, Maguire JJ, Davenport AP. Expression of the apelin receptor, a novel potential therapeutic target, and its endogenous ligands in diverse stem cell populations in human glioblastoma. Front Neurosci 2024; 18:1379658. [PMID: 38803685 PMCID: PMC11128631 DOI: 10.3389/fnins.2024.1379658] [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: 01/31/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024] Open
Abstract
Glioblastoma multiforme (GBM) is one of the most common and lethal forms of brain cancer, carrying a very poor prognosis (median survival of ~15 months post-diagnosis). Treatment typically involves invasive surgical resection of the tumour mass, followed by radiotherapy and adjuvant chemotherapy using the alkylating agent temozolomide, but over half of patients do not respond to this drug and considerable resistance is observed. Tumour heterogeneity is the main cause of therapeutic failure, where diverse progenitor glioblastoma stem cell (GSC) lineages in the microenvironment drive tumour recurrence and therapeutic resistance. The apelin receptor is a class A GPCR that binds two endogenous peptide ligands, apelin and ELA, and plays a role in the proliferation and survival of cancer cells. Here, we used quantitative whole slide immunofluorescent imaging of human GBM samples to characterise expression of the apelin receptor and both its ligands in the distinct GSC lineages, namely neural-progenitor-like cells (NPCs), oligodendrocyte-progenitor-like cells (OPCs), and mesenchymal-like cells (MES), as well as reactive astrocytic cells. The data confirm the presence of the apelin receptor as a tractable drug target that is common across the key cell populations driving tumour growth and maintenance, offering a potential novel therapeutic approach for patients with GBM.
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Affiliation(s)
- Thomas L. Williams
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Peter Nwokoye
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Rhoda E. Kuc
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Kieran Smith
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Anna L. Paterson
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Kieren Allinson
- Department of Pathology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, United Kingdom
| | - Janet J. Maguire
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | - Anthony P. Davenport
- Experimental Medicine and Immunotherapeutics, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
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11
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Bumbaca B, Birtwistle MR, Gallo JM. Network Analyses of Brain Tumor Patients' Multiomic Data Reveals Pharmacological Opportunities to Alter Cell State Transitions. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.08.593202. [PMID: 38766170 PMCID: PMC11100715 DOI: 10.1101/2024.05.08.593202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Glioblastoma Multiforme (GBM) remains a particularly difficult cancer to treat, and survival outcomes remain poor. In addition to the lack of dedicated drug discovery programs for GBM, extensive intratumor heterogeneity and epigenetic plasticity related to cell-state transitions are major roadblocks to successful drug therapy in GBM. To study these phenomenon, publicly available snRNAseq and bulk RNAseq data from patient samples were used to categorize cells from patients into four cell states (i.e. phenotypes), namely: (i) neural progenitor-like (NPC-like), (ii) oligodendrocyte progenitor-like (OPC-like), (iii) astrocyte-like (AC-like), and (iv) mesenchymal-like (MES-like). Patients were subsequently grouped into subpopulations based on which cell-state was the most dominant in their respective tumor. By incorporating phosphoproteomic measurements from the same patients, a protein-protein interaction network (PPIN) was constructed for each cell state. These four-cell state PPINs were pooled to form a single Boolean network that was used for in silico protein knockout simulations to investigate mechanisms that either promote or prevent cell state transitions. Simulation results were input into a boosted tree machine learning model which predicted the cell states or phenotypes of GBM patients from an independent public data source, the Glioma Longitudinal Analysis (GLASS) Consortium. Combining the simulation results and the machine learning predictions, we generated hypotheses for clinically relevant causal mechanisms of cell state transitions. For example, the transcription factor TFAP2A can be seen to promote a transition from the NPC-like to the MES-like state. Such protein nodes and the associated signaling pathways provide potential drug targets that can be further tested in vitro and support cell state-directed (CSD) therapy.
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Affiliation(s)
- Brandon Bumbaca
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo NY, USA
| | - Marc R Birtwistle
- Department of Chemical and Biomolecular Engineering, Clemson University, Clemson SC, USA
- Department of Bioengineering, Clemson University, Clemson SC, USA
| | - James M Gallo
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo NY, USA
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12
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Johnson AL, Lopez-Bertoni H. Cellular diversity through space and time: adding new dimensions to GBM therapeutic development. Front Genet 2024; 15:1356611. [PMID: 38774283 PMCID: PMC11106394 DOI: 10.3389/fgene.2024.1356611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 04/15/2024] [Indexed: 05/24/2024] Open
Abstract
The current median survival for glioblastoma (GBM) patients is only about 16 months, with many patients succumbing to the disease in just a matter of months, making it the most common and aggressive primary brain cancer in adults. This poor outcome is, in part, due to the lack of new treatment options with only one FDA-approved treatment in the last decade. Advances in sequencing techniques and transcriptomic analyses have revealed a vast degree of heterogeneity in GBM, from inter-patient diversity to intra-tumoral cellular variability. These cutting-edge approaches are providing new molecular insights highlighting a critical role for the tumor microenvironment (TME) as a driver of cellular plasticity and phenotypic heterogeneity. With this expanded molecular toolbox, the influence of TME factors, including endogenous (e.g., oxygen and nutrient availability and interactions with non-malignant cells) and iatrogenically induced (e.g., post-therapeutic intervention) stimuli, on tumor cell states can be explored to a greater depth. There exists a critical need for interrogating the temporal and spatial aspects of patient tumors at a high, cell-level resolution to identify therapeutically targetable states, interactions and mechanisms. In this review, we discuss advancements in our understanding of spatiotemporal diversity in GBM with an emphasis on the influence of hypoxia and immune cell interactions on tumor cell heterogeneity. Additionally, we describe specific high-resolution spatially resolved methodologies and their potential to expand the impact of pre-clinical GBM studies. Finally, we highlight clinical attempts at targeting hypoxia- and immune-related mechanisms of malignancy and the potential therapeutic opportunities afforded by single-cell and spatial exploration of GBM patient specimens.
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Affiliation(s)
- Amanda L. Johnson
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Baltimore, MD, United States
| | - Hernando Lopez-Bertoni
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Baltimore, MD, United States
- Oncology, Baltimore, MD, United States
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University School of Medicine, Baltimore, MD, United States
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13
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Voigtlaender S, Pawelczyk J, Geiger M, Vaios EJ, Karschnia P, Cudkowicz M, Dietrich J, Haraldsen IRJH, Feigin V, Owolabi M, White TL, Świeboda P, Farahany N, Natarajan V, Winter SF. Artificial intelligence in neurology: opportunities, challenges, and policy implications. J Neurol 2024; 271:2258-2273. [PMID: 38367046 DOI: 10.1007/s00415-024-12220-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/20/2024] [Accepted: 01/22/2024] [Indexed: 02/19/2024]
Abstract
Neurological conditions are the leading cause of disability and mortality combined, demanding innovative, scalable, and sustainable solutions. Brain health has become a global priority with adoption of the World Health Organization's Intersectoral Global Action Plan in 2022. Simultaneously, rapid advancements in artificial intelligence (AI) are revolutionizing neurological research and practice. This scoping review of 66 original articles explores the value of AI in neurology and brain health, systematizing the landscape for emergent clinical opportunities and future trends across the care trajectory: prevention, risk stratification, early detection, diagnosis, management, and rehabilitation. AI's potential to advance personalized precision neurology and global brain health directives hinges on resolving core challenges across four pillars-models, data, feasibility/equity, and regulation/innovation-through concerted pursuit of targeted recommendations. Paramount actions include swift, ethical, equity-focused integration of novel technologies into clinical workflows, mitigating data-related issues, counteracting digital inequity gaps, and establishing robust governance frameworks balancing safety and innovation.
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Affiliation(s)
- Sebastian Voigtlaender
- Systems Neuroscience Division, Max-Planck-Institute for Biological Cybernetics, Tübingen, Germany
- Virtual Diagnostics Team, QuantCo Inc., Cambridge, MA, USA
| | - Johannes Pawelczyk
- Faculty of Medicine, Ruprecht-Karls-University, Heidelberg, Germany
- Graduate Center of Medicine and Health, Technical University Munich, Munich, Germany
| | - Mario Geiger
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- NVIDIA, Zurich, Switzerland
| | - Eugene J Vaios
- Department of Radiation Oncology, Duke University Medical Center, Durham, NC, USA
| | - Philipp Karschnia
- Department of Neurosurgery, Ludwig-Maximilians-University and University Hospital Munich, Munich, Germany
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Merit Cudkowicz
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jorg Dietrich
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Ira R J Hebold Haraldsen
- Department of Neurology, Division of Clinical Neuroscience, Oslo University Hospital, Oslo, Norway
| | - Valery Feigin
- National Institute for Stroke and Applied Neurosciences, Auckland University of Technology, Auckland, New Zealand
| | - Mayowa Owolabi
- Center for Genomics and Precision Medicine, College of Medicine, University of Ibadan, Ibadan, Nigeria
- Neurology Unit, Department of Medicine, University of Ibadan, Ibadan, Nigeria
- Blossom Specialist Medical Center, Ibadan, Nigeria
- Lebanese American University of Beirut, Beirut, Lebanon
| | - Tara L White
- Department of Behavioral and Social Sciences, Brown University, Providence, RI, USA
| | | | | | | | - Sebastian F Winter
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.
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14
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Khalighi S, Reddy K, Midya A, Pandav KB, Madabhushi A, Abedalthagafi M. Artificial intelligence in neuro-oncology: advances and challenges in brain tumor diagnosis, prognosis, and precision treatment. NPJ Precis Oncol 2024; 8:80. [PMID: 38553633 PMCID: PMC10980741 DOI: 10.1038/s41698-024-00575-0] [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: 10/19/2023] [Accepted: 03/13/2024] [Indexed: 04/02/2024] Open
Abstract
This review delves into the most recent advancements in applying artificial intelligence (AI) within neuro-oncology, specifically emphasizing work on gliomas, a class of brain tumors that represent a significant global health issue. AI has brought transformative innovations to brain tumor management, utilizing imaging, histopathological, and genomic tools for efficient detection, categorization, outcome prediction, and treatment planning. Assessing its influence across all facets of malignant brain tumor management- diagnosis, prognosis, and therapy- AI models outperform human evaluations in terms of accuracy and specificity. Their ability to discern molecular aspects from imaging may reduce reliance on invasive diagnostics and may accelerate the time to molecular diagnoses. The review covers AI techniques, from classical machine learning to deep learning, highlighting current applications and challenges. Promising directions for future research include multimodal data integration, generative AI, large medical language models, precise tumor delineation and characterization, and addressing racial and gender disparities. Adaptive personalized treatment strategies are also emphasized for optimizing clinical outcomes. Ethical, legal, and social implications are discussed, advocating for transparency and fairness in AI integration for neuro-oncology and providing a holistic understanding of its transformative impact on patient care.
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Affiliation(s)
- Sirvan Khalighi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Kartik Reddy
- Department of Radiology, Emory University, Atlanta, GA, USA
| | - Abhishek Midya
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Krunal Balvantbhai Pandav
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA
| | - Anant Madabhushi
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA.
- Atlanta Veterans Administration Medical Center, Atlanta, GA, USA.
| | - Malak Abedalthagafi
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA.
- The Cell and Molecular Biology Program, Winship Cancer Institute, Atlanta, GA, USA.
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15
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Sussman JH, Oldridge DA, Yu W, Chen CH, Zellmer AM, Rong J, Parvaresh-Rizi A, Thadi A, Xu J, Bandyopadhyay S, Sun Y, Wu D, Emerson Hunter C, Brosius S, Ahn KJ, Baxter AE, Koptyra MP, Vanguri RS, McGrory S, Resnick AC, Storm PB, Amankulor NM, Santi M, Viaene AN, Zhang N, Raedt TD, Cole K, Tan K. A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.06.583588. [PMID: 38496580 PMCID: PMC10942465 DOI: 10.1101/2024.03.06.583588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Pediatric high-grade glioma (pHGG) is an incurable central nervous system malignancy that is a leading cause of pediatric cancer death. While pHGG shares many similarities to adult glioma, it is increasingly recognized as a molecularly distinct, yet highly heterogeneous disease. In this study, we longitudinally profiled a molecularly diverse cohort of 16 pHGG patients before and after standard therapy through single-nucleus RNA and ATAC sequencing, whole-genome sequencing, and CODEX spatial proteomics to capture the evolution of the tumor microenvironment during progression following treatment. We found that the canonical neoplastic cell phenotypes of adult glioblastoma are insufficient to capture the range of tumor cell states in a pediatric cohort and observed differential tumor-myeloid interactions between malignant cell states. We identified key transcriptional regulators of pHGG cell states and did not observe the marked proneural to mesenchymal shift characteristic of adult glioblastoma. We showed that essential neuromodulators and the interferon response are upregulated post-therapy along with an increase in non-neoplastic oligodendrocytes. Through in vitro pharmacological perturbation, we demonstrated novel malignant cell-intrinsic targets. This multiomic atlas of longitudinal pHGG captures the key features of therapy response that support distinction from its adult counterpart and suggests therapeutic strategies which are targeted to pediatric gliomas.
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Affiliation(s)
- Jonathan H. Sussman
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Derek A. Oldridge
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Wenbao Yu
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman
School of Medicine, Philadelphia, PA
| | - Chia-Hui Chen
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
| | - Abigail M. Zellmer
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Jiazhen Rong
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
- Department of Statistics and Data Science, University of
Pennsylvania, Philadelphia, PA
| | | | - Anusha Thadi
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
| | - Jason Xu
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Shovik Bandyopadhyay
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Cellular and Molecular Biology Graduate Group, Perelman School of
Medicine, University of Pennsylvania, PA
| | - Yusha Sun
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Neuroscience Graduate Group, Perelman School of Medicine,
University of Pennsylvania, PA
| | - David Wu
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - C. Emerson Hunter
- Medical Scientist Training Program, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Stephanie Brosius
- Graduate Group in Genomics and Computational Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Kyung Jin Ahn
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
| | - Amy E. Baxter
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Mateusz P. Koptyra
- Department of Neurosurgery, Children’s Hospital of
Philadelphia, Philadelphia, PA
| | - Rami S. Vanguri
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Stephanie McGrory
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
| | - Adam C. Resnick
- Department of Neurosurgery, Children’s Hospital of
Philadelphia, Philadelphia, PA
| | - Phillip B. Storm
- Department of Neurosurgery, Children’s Hospital of
Philadelphia, Philadelphia, PA
| | - Nduka M. Amankulor
- Department of Neurosurgery, Perelman School of Medicine,
Philadelphia, PA
| | - Mariarita Santi
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Angela N. Viaene
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Nancy Zhang
- Department of Statistics and Data Science, University of
Pennsylvania, Philadelphia, PA
| | - Thomas De Raedt
- Department of Pathology and Laboratory Medicine, Perelman School
of Medicine at the University of Pennsylvania, Philadelphia, PA
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
| | - Kristina Cole
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman
School of Medicine, Philadelphia, PA
| | - Kai Tan
- Center for Childhood Cancer Research, Children’s Hospital
of Philadelphia, Philadelphia, PA
- Department of Pediatrics, University of Pennsylvania Perelman
School of Medicine, Philadelphia, PA
- Center for Single Cell Biology, Children’s Hospital of
Philadelphia, Philadelphia, PA
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16
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Zheng Y, Pizurica M, Carrillo-Perez F, Noor H, Yao W, Wohlfart C, Marchal K, Vladimirova A, Gevaert O. Digital profiling of cancer transcriptomes from histology images with grouped vision attention. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.09.28.560068. [PMID: 37808782 PMCID: PMC10557714 DOI: 10.1101/2023.09.28.560068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Cancer is a heterogeneous disease that demands precise molecular profiling for better understanding and management. Recently, deep learning has demonstrated potentials for cost-efficient prediction of molecular alterations from histology images. While transformer-based deep learning architectures have enabled significant progress in non-medical domains, their application to histology images remains limited due to small dataset sizes coupled with the explosion of trainable parameters. Here, we develop SEQUOIA, a transformer model to predict cancer transcriptomes from whole-slide histology images. To enable the full potential of transformers, we first pre-train the model using data from 1,802 normal tissues. Then, we fine-tune and evaluate the model in 4,331 tumor samples across nine cancer types. The prediction performance is assessed at individual gene levels and pathway levels through Pearson correlation analysis and root mean square error. The generalization capacity is validated across two independent cohorts comprising 1,305 tumors. In predicting the expression levels of 25,749 genes, the highest performance is observed in cancers from breast, kidney and lung, where SEQUOIA accurately predicts the expression of 11,069, 10,086 and 8,759 genes, respectively. The accurately predicted genes are associated with the regulation of inflammatory response, cell cycles and metabolisms. While the model is trained at the tissue level, we showcase its potential in predicting spatial gene expression patterns using spatial transcriptomics datasets. Leveraging the prediction performance, we develop a digital gene expression signature that predicts the risk of recurrence in breast cancer. SEQUOIA deciphers clinically relevant gene expression patterns from histology images, opening avenues for improved cancer management and personalized therapies.
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Affiliation(s)
- Yuanning Zheng
- Department of Medicine, Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, Stanford, 94305, USA
| | - Marija Pizurica
- Department of Medicine, Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, Stanford, 94305, USA
- Internet technology and Data science Lab (IDLab), Ghent University, Technologiepark-Zwijnaarde 126, Ghent, 9052, Gent, Belgium
| | - Francisco Carrillo-Perez
- Department of Medicine, Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, Stanford, 94305, USA
| | - Humaira Noor
- Department of Medicine, Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, Stanford, 94305, USA
| | - Wei Yao
- Roche Information Solutions, Roche Diagnostics Corporation, Santa Clara, California, USA
| | | | - Kathleen Marchal
- Internet technology and Data science Lab (IDLab), Ghent University, Technologiepark-Zwijnaarde 126, Ghent, 9052, Gent, Belgium
| | - Antoaneta Vladimirova
- Roche Information Solutions, Roche Diagnostics Corporation, Santa Clara, California, USA
| | - Olivier Gevaert
- Department of Medicine, Stanford Center for Biomedical Informatics Research (BMIR), Stanford University, Stanford, 94305, USA
- Department of Biomedical Data Science, Stanford University, Stanford, 94305, USA
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17
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Huang R, Lu X, Sun X, Wu H. A novel immune cell signature for predicting glioblastoma after radiotherapy prognosis and guiding therapy. Int J Immunopathol Pharmacol 2024; 38:3946320241249395. [PMID: 38687369 PMCID: PMC11062235 DOI: 10.1177/03946320241249395] [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: 09/27/2023] [Accepted: 03/28/2024] [Indexed: 05/02/2024] Open
Abstract
Background: Glioblastoma, a highly aggressive brain tumor, poses a significant clinical challenge, particularly in the context of radiotherapy. In this study, we aimed to explore infiltrating immune cells and identify immune-related genes associated with glioblastoma radiotherapy prognosis. Subsequently, we constructed a signature based on these genes to discern differences in molecular and tumor microenvironment immune characteristics, ultimately informing potential therapeutic strategies for patients with varying risk profiles. Methods: We leveraged UCSC Xena and CGGA gene expression profiles from post-radiotherapy glioblastoma as verification cohorts. Infiltration ratios were stratified into high and low groups based on the median value. Differential gene expression was determined through Limma differential analysis. A signature comprising four genes was constructed, guided by Gene Ontology (GO) functional enrichment results and Kaplan-Meier survival analysis. We evaluated differences in cell infiltration levels, Immune Score, Stromal Score, and ESTIMATE Score and their Pearson correlations with the signature. Spearman's correlation was computed between the signature and patient drug sensitivity (IC50), predicted using Genomics of Drug Sensitivity in Cancer (GDSC) and CCLE databases. Results: Notably, the infiltration of central memory CD8+T cells exhibited a significant correlation with glioblastoma radiotherapy prognosis. Samples were dichotomized into high- and low-risk groups based on the optimal signature threshold (2.466642). Kaplan-Meier (K-M) survival analysis revealed that the high-risk group experienced a significantly poorer prognosis (p = .0068), with AUC values exceeding 0.82 at 1, 3, and 5 years, underscoring the robust predictive potential of the signature scoring system. Independent validation sets substantiated the validity of the signature. Statistically significant differences in tumor microenvironments (p < .05) were observed between high- and low-risk groups, and these differences were significantly correlated with the signature (p < .05). Furthermore, there were significant correlations between high and low-risk groups regarding immune checkpoint expressions, Immune Prognostic Score (IPS), and Tumor Immune Dysfunction and Exclusion (TIDE) scores. Conclusion: The immune cell signature, comprising SDC-1, PLAUR, FN1, and CXCL13, holds promise as a predictive tool for assessing glioblastoma prognosis following radiotherapy. This signature also offers valuable guidance for tailoring treatment strategies, emphasizing its potential clinical relevance in improving patient outcomes.
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Affiliation(s)
- Rong Huang
- Department of Radiation Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Xiaoxu Lu
- Department of Radiation Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Xueming Sun
- Department of Radiation Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
| | - Hui Wu
- Department of Radiation Oncology, The Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, China
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Genoud V, Kinnersley B, Brown NF, Ottaviani D, Mulholland P. Therapeutic Targeting of Glioblastoma and the Interactions with Its Microenvironment. Cancers (Basel) 2023; 15:5790. [PMID: 38136335 PMCID: PMC10741850 DOI: 10.3390/cancers15245790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/01/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Glioblastoma (GBM) is the most common primary malignant brain tumour, and it confers a dismal prognosis despite intensive multimodal treatments. Whilst historically, research has focussed on the evolution of GBM tumour cells themselves, there is growing recognition of the importance of studying the tumour microenvironment (TME). Improved characterisation of the interaction between GBM cells and the TME has led to a better understanding of therapeutic resistance and the identification of potential targets to block these escape mechanisms. This review describes the network of cells within the TME and proposes treatment strategies for simultaneously targeting GBM cells, the surrounding immune cells, and the crosstalk between them.
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Affiliation(s)
- Vassilis Genoud
- Glioblastoma Research Group, University College London, London WC1E 6DD, UK (B.K.)
- Department of Oncology, University College London Hospitals, London NW1 2PB, UK
- Department of Oncology, University Hospitals of Geneva, 1205 Geneva, Switzerland
- Centre for Translational Research in Onco-Haematology, University of Geneva, 1205 Geneva, Switzerland
| | - Ben Kinnersley
- Glioblastoma Research Group, University College London, London WC1E 6DD, UK (B.K.)
- Department of Oncology, University College London Hospitals, London NW1 2PB, UK
| | - Nicholas F. Brown
- Glioblastoma Research Group, University College London, London WC1E 6DD, UK (B.K.)
- Guy’s Cancer, Guy’s & St Thomas’ NHS Foundation Trust, London SE1 3SS, UK
| | - Diego Ottaviani
- Glioblastoma Research Group, University College London, London WC1E 6DD, UK (B.K.)
- Department of Oncology, University College London Hospitals, London NW1 2PB, UK
| | - Paul Mulholland
- Glioblastoma Research Group, University College London, London WC1E 6DD, UK (B.K.)
- Department of Oncology, University College London Hospitals, London NW1 2PB, UK
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Nussinov R, Liu Y, Zhang W, Jang H. Cell phenotypes can be predicted from propensities of protein conformations. Curr Opin Struct Biol 2023; 83:102722. [PMID: 37871498 PMCID: PMC10841533 DOI: 10.1016/j.sbi.2023.102722] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/26/2023] [Accepted: 09/27/2023] [Indexed: 10/25/2023]
Abstract
Proteins exist as dynamic conformational ensembles. Here we suggest that the propensities of the conformations can be predictors of cell function. The conformational states that the molecules preferentially visit can be viewed as phenotypic determinants, and their mutations work by altering the relative propensities, thus the cell phenotype. Our examples include (i) inactive state variants harboring cancer driver mutations that present active state-like conformational features, as in K-Ras4BG12V compared to other K-Ras4BG12X mutations; (ii) mutants of the same protein presenting vastly different phenotypic and clinical profiles: cancer and neurodevelopmental disorders; (iii) alterations in the occupancies of the conformational (sub)states influencing enzyme reactivity. Thus, protein conformational propensities can determine cell fate. They can also suggest the allosteric drugs efficiency.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel; Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA.
| | - Yonglan Liu
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Wengang Zhang
- Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Cancer Innovation Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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Davis S, Scott C, Oetjen J, Charles PD, Kessler BM, Ansorge O, Fischer R. Deep topographic proteomics of a human brain tumour. Nat Commun 2023; 14:7710. [PMID: 38001067 PMCID: PMC10673928 DOI: 10.1038/s41467-023-43520-8] [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: 03/01/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
The spatial organisation of cellular protein expression profiles within tissue determines cellular function and is key to understanding disease pathology. To define molecular phenotypes in the spatial context of tissue, there is a need for unbiased, quantitative technology capable of mapping proteomes within tissue structures. Here, we present a workflow for spatially-resolved, quantitative proteomics of tissue that generates maps of protein abundance across tissue slices derived from a human atypical teratoid-rhabdoid tumour at three spatial resolutions, the highest being 40 µm, to reveal distinct abundance patterns of thousands of proteins. We employ spatially-aware algorithms that do not require prior knowledge of the fine tissue structure to detect proteins and pathways with spatial abundance patterns and correlate proteins in the context of tissue heterogeneity and cellular features such as extracellular matrix or proximity to blood vessels. We identify PYGL, ASPH and CD45 as spatial markers for tumour boundary and reveal immune response-driven, spatially-organised protein networks of the extracellular tumour matrix. Overall, we demonstrate spatially-aware deep proteo-phenotyping of tissue heterogeneity, to re-define understanding tissue biology and pathology at the molecular level.
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Affiliation(s)
- Simon Davis
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Connor Scott
- Academic Unit of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Janina Oetjen
- Bruker Daltonics GmbH & Co. KG, Fahrenheitstraße 4, 28359, Bremen, Germany
| | - Philip D Charles
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Big Data Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Benedikt M Kessler
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK
| | - Olaf Ansorge
- Academic Unit of Neuropathology, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Roman Fischer
- Target Discovery Institute, Centre for Medicines Discovery, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
- Chinese Academy for Medical Sciences Oxford Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford, OX3 7FZ, UK.
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Fatemi MY, Lu Y, Diallo AB, Srinivasan G, Azher ZL, Christensen BC, Salas LA, Tsongalis GJ, Palisoul SM, Perreard L, Kolling FW, Vaickus LJ, Levy JJ. The Overlooked Role of Specimen Preparation in Bolstering Deep Learning-Enhanced Spatial Transcriptomics Workflows. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.09.23296700. [PMID: 37873287 PMCID: PMC10593052 DOI: 10.1101/2023.10.09.23296700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The application of deep learning methods to spatial transcriptomics has shown promise in unraveling the complex relationships between gene expression patterns and tissue architecture as they pertain to various pathological conditions. Deep learning methods that can infer gene expression patterns directly from tissue histomorphology can expand the capability to discern spatial molecular markers within tissue slides. However, current methods utilizing these techniques are plagued by substantial variability in tissue preparation and characteristics, which can hinder the broader adoption of these tools. Furthermore, training deep learning models using spatial transcriptomics on small study cohorts remains a costly endeavor. Necessitating novel tissue preparation processes enhance assay reliability, resolution, and scalability. This study investigated the impact of an enhanced specimen processing workflow for facilitating a deep learning-based spatial transcriptomics assessment. The enhanced workflow leveraged the flexibility of the Visium CytAssist assay to permit automated H&E staining (e.g., Leica Bond) of tissue slides, whole-slide imaging at 40x-resolution, and multiplexing of tissue sections from multiple patients within individual capture areas for spatial transcriptomics profiling. Using a cohort of thirteen pT3 stage colorectal cancer (CRC) patients, we compared the efficacy of deep learning models trained on slide prepared using an enhanced workflow as compared to the traditional workflow which leverages manual tissue staining and standard imaging of tissue slides. Leveraging Inceptionv3 neural networks, we aimed to predict gene expression patterns across matched serial tissue sections, each stemming from a distinct workflow but aligned based on persistent histological structures. Findings indicate that the enhanced workflow considerably outperformed the traditional spatial transcriptomics workflow. Gene expression profiles predicted from enhanced tissue slides also yielded expression patterns more topologically consistent with the ground truth. This led to enhanced statistical precision in pinpointing biomarkers associated with distinct spatial structures. These insights can potentially elevate diagnostic and prognostic biomarker detection by broadening the range of spatial molecular markers linked to metastasis and recurrence. Future endeavors will further explore these findings to enrich our comprehension of various diseases and uncover molecular pathways with greater nuance. Combining deep learning with spatial transcriptomics provides a compelling avenue to enrich our understanding of tumor biology and improve clinical outcomes. For results of the highest fidelity, however, effective specimen processing is crucial, and fostering collaboration between histotechnicians, pathologists, and genomics specialists is essential to herald this new era in spatial transcriptomics-driven cancer research.
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