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Zuccato JA, Mamatjan Y, Nassiri F, Ajisebutu A, Liu JC, Muazzam A, Singh O, Zhang W, Voisin M, Mirhadi S, Suppiah S, Wybenga-Groot L, Tajik A, Simpson C, Saarela O, Tsao MS, Kislinger T, Aldape KD, Moran MF, Patil V, Zadeh G. Prediction of brain metastasis development with DNA methylation signatures. Nat Med 2024:10.1038/s41591-024-03286-y. [PMID: 39379704 DOI: 10.1038/s41591-024-03286-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Accepted: 09/05/2024] [Indexed: 10/10/2024]
Abstract
Brain metastases (BMs) are the most common and among the deadliest brain tumors. Currently, there are no reliable predictors of BM development from primary cancer, which limits early intervention. Lung adenocarcinoma (LUAD) is the most common BM source and here we obtained 402 tumor and plasma samples from a large cohort of patients with LUAD with or without BM (n = 346). LUAD DNA methylation signatures were evaluated to build and validate an accurate model predicting BM development from LUAD, which was integrated with clinical factors to provide comprehensive patient-specific BM risk probabilities in a nomogram. Additionally, immune and cell interaction gene sets were differentially methylated at promoters in BM versus paired primary LUAD and had aligning dysregulation in the proteome. Immune cells were differentially abundant in BM versus LUAD. Finally, liquid biomarkers identified from methylated cell-free DNA sequenced in plasma were used to generate and validate accurate classifiers for early BM detection. Overall, LUAD methylomes can be leveraged to predict and noninvasively identify BM, moving toward improved patient outcomes with personalized treatment.
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Affiliation(s)
- Jeffrey A Zuccato
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Yasin Mamatjan
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- The Faculty of Science, Thompson Rivers University, Kamloops, BC, Canada
| | - Farshad Nassiri
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Andrew Ajisebutu
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Jeffrey C Liu
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Ammara Muazzam
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Olivia Singh
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
| | - Wen Zhang
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Mathew Voisin
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Shideh Mirhadi
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Suganth Suppiah
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Leanne Wybenga-Groot
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- SPARC BioCentre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alireza Tajik
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada
- School of Medicine, St. George's University, Grenada, Grenada
| | - Craig Simpson
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- SPARC BioCentre, Hospital for Sick Children, Toronto, Ontario, Canada
| | - Olli Saarela
- Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada
| | - Ming S Tsao
- Department of Pathology, The Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Kenneth D Aldape
- Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Michael F Moran
- Program in Cell Biology, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Vikas Patil
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada.
| | - Gelareh Zadeh
- MacFeeters Hamilton Neuro-Oncology Program, Princess Margaret Cancer Centre, University Health Network and University of Toronto, Toronto, Ontario, Canada.
- Division of Neurosurgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada.
- The Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, Ontario, Canada.
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Koh YW, Han JH, Haam S, Lee HW. Changes in the expression of cell interaction-related pathways during brain metastasis in lung adenocarcinoma: Gene expression and immunohistochemical analysis. Pathol Res Pract 2024; 260:155375. [PMID: 38878665 DOI: 10.1016/j.prp.2024.155375] [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: 12/21/2023] [Accepted: 05/28/2024] [Indexed: 08/09/2024]
Abstract
BACKGROUND Brain metastasis (BM) is a prevalent prognostic event in the development of lung adenocarcinoma (LUAD) with a poor prognosis. Alterations in gene or protein expression during various phases of BM remain unclear. METHODS We performed gene expression and pathway analyses using a metastasis-related gene panel on 12 lung tissues from patients with confirmed BM, 12 lung tissues from patients without BM, and 12 matched brain tissues from patients with confirmed BM during follow-up after LUAD surgery. The results of the gene expression analysis were validated by immunohistochemistry. RESULTS Cell interaction-related pathways (such as focal adhesion, extracellular matrix-receptor interaction, and proteoglycans in cancer) showed the greatest differences among the three groups. Expression of the cell interaction-related pathway was highest in the lung sample of BM group and lowest in the matched brain tissue. Using a machine learning model, a signature of 20 genes from cell interaction-related pathways accurately predicted BM (area under the curve score of 0.792 and an accuracy rate of 0.875). Immunohistochemical analysis showed higher expression of proteins associated with cell interaction-related genes and a mesenchymal phenotype in the lung sample of BM group than in those without BM or matched brain tissue. CONCLUSIONS LUAD acquires the characteristics of the cell interaction-related pathway that leads to the development of BM, with a significant decrease in expression following brain colonization.
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Affiliation(s)
- Young Wha Koh
- Department of Pathology, Ajou University School of Medicine, Suwon-si, South Korea.
| | - Jae-Ho Han
- Department of Pathology, Ajou University School of Medicine, Suwon-si, South Korea
| | - Seokjin Haam
- Department of Thoracic and Cardiovascular Surgery, Ajou University School of Medicine, Suwon-si, South Korea
| | - Hyun Woo Lee
- Department of Hematology-Oncology, Ajou University School of Medicine, Suwon-si, South Korea
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Chen Y, Chen XS, He RQ, Huang ZG, Lu HP, Huang H, Yang DP, Tang ZQ, Yang X, Zhang HJ, Qv N, Kong JL, Chen G. What enlightenment has the development of lung cancer bone metastasis brought in the last 22 years. World J Clin Oncol 2024; 15:765-782. [PMID: 38946828 PMCID: PMC11212609 DOI: 10.5306/wjco.v15.i6.765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 05/01/2024] [Accepted: 05/22/2024] [Indexed: 06/24/2024] Open
Abstract
BACKGROUND Lung cancer bone metastasis (LCBM) is a disease with a poor prognosis, high risk and large patient population. Although considerable scientific output has accumulated on LCBM, problems have emerged, such as confusing research structures. AIM To organize the research frontiers and body of knowledge of the studies on LCBM from the last 22 years according to their basic research and translation, clinical treatment, and clinical diagnosis to provide a reference for the development of new LCBM clinical and basic research. METHODS We used tools, including R, VOSviewer and CiteSpace software, to measure and visualize the keywords and other metrics of 1903 articles from the Web of Science Core Collection. We also performed enrichment and protein-protein interaction analyses of gene expression datasets from LCBM cases worldwide. RESULTS Research on LCBM has received extensive attention from scholars worldwide over the last 20 years. Targeted therapies and immunotherapies have evolved into the mainstream basic and clinical research directions. The basic aspects of drug resistance mechanisms and parathyroid hormone-related protein may provide new ideas for mechanistic study and improvements in LCBM prognosis. The produced molecular map showed that ribosomes and focal adhesion are possible pathways that promote LCBM occurrence. CONCLUSION Novel therapies for LCBM face animal testing and drug resistance issues. Future focus should centre on advancing clinical therapies and researching drug resistance mechanisms and ribosome-related pathways.
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Affiliation(s)
- Yi Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Xiao-Song Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Rong-Quan He
- Department of Medical Oncology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Zhi-Guang Huang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Hui-Ping Lu
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Hong Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Da-Ping Yang
- Department of Pathology, Guigang People’s Hospital of Guangxi/The Eighth Affiliated Hospital of Guangxi Medical University, Guigang 537100, Guangxi Zhuang Autonomous Region, China
| | - Zhong-Qing Tang
- Department of Pathology, Wuzhou Gongren Hospital/The Seventh Affiliated Hospital of Guangxi Medical University, Wuzhou 543000, Guangxi Zhuang Autonomous Region, China
| | - Xia Yang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Han-Jie Zhang
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Ning Qv
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Jin-Liang Kong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
| | - Gang Chen
- Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, China
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Wen J, Yu JZ, Liu C, Ould Ismail AAO, Ma W. Exploring the Molecular Tumor Microenvironment and Translational Biomarkers in Brain Metastases of Non-Small-Cell Lung Cancer. Int J Mol Sci 2024; 25:2044. [PMID: 38396722 PMCID: PMC10889194 DOI: 10.3390/ijms25042044] [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: 12/05/2023] [Revised: 01/17/2024] [Accepted: 02/01/2024] [Indexed: 02/25/2024] Open
Abstract
Brain metastases represent a significant clinical challenge in the treatment of non-small-cell lung cancer (NSCLC), often leading to a severe decline in patient prognosis and survival. Recent advances in imaging and systemic treatments have increased the detection rates of brain metastases, yet clinical outcomes remain dismal due to the complexity of the metastatic tumor microenvironment (TME) and the lack of specific biomarkers for early detection and targeted therapy. The intricate interplay between NSCLC tumor cells and the surrounding TME in brain metastases is pivotal, influencing tumor progression, immune evasion, and response to therapy. This underscores the necessity for a deeper understanding of the molecular underpinnings of brain metastases, tumor microenvironment, and the identification of actionable biomarkers that can inform multimodal treatment approaches. The goal of this review is to synthesize current insights into the TME and elucidate molecular mechanisms in NSCLC brain metastases. Furthermore, we will explore the promising horizon of emerging biomarkers, both tissue- and liquid-based, that hold the potential to radically transform the treatment strategies and the enhancement of patient outcomes.
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Affiliation(s)
- Jiexi Wen
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Jie-Zeng Yu
- Division of Hematology/Oncology, Department of Medicine, University of California at San Francisco, San Francisco, CA 94143, USA
| | - Catherine Liu
- School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
| | - A. Aziz O. Ould Ismail
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
| | - Weijie Ma
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Geisel School of Medicine at Dartmouth, Lebanon, NH 03756, USA
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Pasternack H, Polzer M, Gemoll T, Kümpers C, Sauer T, Lazar-Karsten P, Hinrichs S, Bohnet S, Perner S, Dressler FF, Kirfel J. Proteomic analyses identify HK1 and ATP5A to be overexpressed in distant metastases of lung adenocarcinomas compared to matched primary tumors. Sci Rep 2023; 13:20948. [PMID: 38016997 PMCID: PMC10684588 DOI: 10.1038/s41598-023-47767-5] [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: 06/30/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide with lung adenocarcinoma (LUAD) being the most common type. Genomic studies of LUAD have advanced our understanding of its tumor biology and accelerated targeted therapy. However, the proteomic characteristics of LUAD are still insufficiently explored. The prognosis for lung cancer patients is still mostly determined by the stage of disease at the time of diagnosis. Focusing on late-stage metastatic LUAD with poor prognosis, we compared the proteomic profiles of primary tumors and matched distant metastases to identify relevant and potentially druggable differences. We performed high-performance liquid chromatography (HPLC) and electrospray ionization tandem mass spectrometry (ESI-MS/MS) on a total of 38 FFPE (formalin-fixed and paraffin-embedded) samples. Using differential expression analysis and unsupervised clustering we identified several proteins that were differentially regulated in metastases compared to matched primary tumors. Selected proteins (HK1, ATP5A, SRI and ARHGDIB) were subjected to validation by immunoblotting. Thereby, significant differential expression could be confirmed for HK1 and ATP5A, both upregulated in metastases compared to matched primary tumors. Our findings give a better understanding of tumor progression and metastatic spreads in LUAD but also demonstrate considerable inter-individual heterogeneity on the proteomic level.
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Affiliation(s)
- Helen Pasternack
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Mirjam Polzer
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
- Institute of Legal Medicine, University Hospital Münster, Münster, Germany
| | - Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Christiane Kümpers
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Thorben Sauer
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Pamela Lazar-Karsten
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Sofie Hinrichs
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Sabine Bohnet
- Department of Pulmonology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
| | - Sven Perner
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
- Pathology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
- Institute of Pathology and Hematopathology, Hamburg, Germany
| | - Franz Friedrich Dressler
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany
- Institute of Pathology, Charité -Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Jutta Kirfel
- Institute of Pathology, University Hospital Schleswig-Holstein, Campus Luebeck, Luebeck, Germany.
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Bottom-Up Proteomics: Advancements in Sample Preparation. Int J Mol Sci 2023; 24:ijms24065350. [PMID: 36982423 PMCID: PMC10049050 DOI: 10.3390/ijms24065350] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/28/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Liquid chromatography–tandem mass spectrometry (LC–MS/MS)-based proteomics is a powerful technique for profiling proteomes of cells, tissues, and body fluids. Typical bottom-up proteomic workflows consist of the following three major steps: sample preparation, LC–MS/MS analysis, and data analysis. LC–MS/MS and data analysis techniques have been intensively developed, whereas sample preparation, a laborious process, remains a difficult task and the main challenge in different applications. Sample preparation is a crucial stage that affects the overall efficiency of a proteomic study; however, it is prone to errors and has low reproducibility and throughput. In-solution digestion and filter-aided sample preparation are the typical and widely used methods. In the past decade, novel methods to improve and facilitate the entire sample preparation process or integrate sample preparation and fractionation have been reported to reduce time, increase throughput, and improve reproducibility. In this review, we have outlined the current methods used for sample preparation in proteomics, including on-membrane digestion, bead-based digestion, immobilized enzymatic digestion, and suspension trapping. Additionally, we have summarized and discussed current devices and methods for integrating different steps of sample preparation and peptide fractionation.
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