1
|
Zhou Z, Zhang R, Zhou A, Lv J, Chen S, Zou H, Zhang G, Lin T, Wang Z, Zhang Y, Weng S, Han X, Liu Z. Proteomics appending a complementary dimension to precision oncotherapy. Comput Struct Biotechnol J 2024; 23:1725-1739. [PMID: 38689716 PMCID: PMC11058087 DOI: 10.1016/j.csbj.2024.04.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Recent advances in high-throughput proteomic profiling technologies have facilitated the precise quantification of numerous proteins across multiple specimens concurrently. Researchers have the opportunity to comprehensively analyze the molecular signatures in plentiful medical specimens or disease pattern cell lines. Along with advances in data analysis and integration, proteomics data could be efficiently consolidated and employed to recognize precise elementary molecular mechanisms and decode individual biomarkers, guiding the precision treatment of tumors. Herein, we review a broad array of proteomics technologies and the progress and methods for the integration of proteomics data and further discuss how to better merge proteomics in precision medicine and clinical settings.
Collapse
Affiliation(s)
- Zhaokai Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Ruiqi Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Aoyang Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jinxiang Lv
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Shuang Chen
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Haijiao Zou
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ting Lin
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Zhan Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| |
Collapse
|
2
|
Duan Y, Zhan H, Wang Q, Li B, Gao H, Liu D, Xu Q, Gao X, Liu Z, Gao P, Wei G, Wang Y. Integrated Lactylome Characterization Reveals the Molecular Dynamics of Protein Regulation in Gastrointestinal Cancers. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400227. [PMID: 39018247 DOI: 10.1002/advs.202400227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 05/19/2024] [Indexed: 07/19/2024]
Abstract
Lysine lactylation (Kla) plays a vital role in several physiological processes. However, the cancer-specific modulation of Kla in gastrointestinal (GI) tumors requires systematic elucidation. Here, global lactylome profiling of cancerous and adjacent tissues is conducted from 40 patients with GI cancer and identified 11698 Kla sites. Lactylome integration revealed that Kla affects proteins involved in hallmark cancer processes, including epigenetic rewiring, metabolic perturbations, and genome instability. Moreover, the study revealed pan-cancer patterns of Kla alterations, among which 37 Kla sites are consistently upregulated in all four GI cancers and are involved in gene regulation. It is further verified that lactylation of CBX3 at K10 mediates its interaction of CBX3 with the epigenetic marker H3K9me3 and facilitates GI cancer progression. Overall, this study provides an invaluable resource for understanding the lactylome landscape in GI cancers, which may provide new paths for drug discovery for these devastating diseases.
Collapse
Affiliation(s)
- Yangmiao Duan
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Hanxiang Zhan
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Qin Wang
- Department of Anesthesiology, Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Bohao Li
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Huiru Gao
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, China
| | - Duanrui Liu
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| | - Qinchen Xu
- Department of Clinical Laboratory, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250033, China
| | - Xin Gao
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Zhenya Liu
- Division of Pancreatic Surgery, Department of General Surgery, Qilu Hospital, Shandong University, Jinan, Shandong, 250012, China
| | - Peng Gao
- Key Laboratory for Experimental Teratology of the Ministry of Education and Department of Pathology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Guangwei Wei
- Key Laboratory for Experimental Teratology of the Ministry of Education, Department of Cell Biology, School of Basic Medical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, 250012, China
| | - Yunshan Wang
- Department of Clinical Laboratory, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, 250021, China
| |
Collapse
|
3
|
Huo Z, Duan Y, Zhan D, Xu X, Zheng N, Cai J, Sun R, Wang J, Cheng F, Gao Z, Xu C, Liu W, Dong Y, Ma S, Zhang Q, Zheng Y, Lou L, Kuang D, Chu Q, Qin J, Wang G, Wang Y. Proteomic Stratification of Prognosis and Treatment Options for Small Cell Lung Cancer. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzae033. [PMID: 38961535 DOI: 10.1093/gpbjnl/qzae033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 10/24/2023] [Accepted: 01/22/2024] [Indexed: 07/05/2024]
Abstract
Small cell lung cancer (SCLC) is a highly malignant and heterogeneous cancer with limited therapeutic options and prognosis prediction models. Here, we analyzed formalin-fixed, paraffin-embedded (FFPE) samples of surgical resections by proteomic profiling, and stratified SCLC into three proteomic subtypes (S-I, S-II, and S-III) with distinct clinical outcomes and chemotherapy responses. The proteomic subtyping was an independent prognostic factor and performed better than current tumor-node-metastasis or Veterans Administration Lung Study Group staging methods. The subtyping results could be further validated using FFPE biopsy samples from an independent cohort, extending the analysis to both surgical and biopsy samples. The signatures of the S-II subtype in particular suggested potential benefits from immunotherapy. Differentially overexpressed proteins in S-III, the worst prognostic subtype, allowed us to nominate potential therapeutic targets, indicating that patient selection may bring new hope for previously failed clinical trials. Finally, analysis of an independent cohort of SCLC patients who had received immunotherapy validated the prediction that the S-II patients had better progression-free survival and overall survival after first-line immunotherapy. Collectively, our study provides the rationale for future clinical investigations to validate the current findings for more accurate prognosis prediction and precise treatments.
Collapse
Affiliation(s)
- Zitian Huo
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- National Health Commission Key Laboratory of Respiratory Diseases, Tongji Hosptial, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yaqi Duan
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- National Health Commission Key Laboratory of Respiratory Diseases, Tongji Hosptial, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Dongdong Zhan
- Beijing Pineal Diagnostics Co., Ltd., Beijing 102206, China
| | - Xizhen Xu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Nairen Zheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jing Cai
- Institution of Pathology, The First Affiliated Hospital of Henan University, Kaifeng 475001, China
| | - Ruifang Sun
- Department of Tumor Biobank, Shanxi Cancer Hospital, Taiyuan 030013, China
| | - Jianping Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Chongqing Key Laboratory of Big Data for Bio Intelligence, School of Bioinformation, Chongqing University of Posts and Telecommunications, Chongqing 400065, China
| | - Fang Cheng
- Beijing Pineal Diagnostics Co., Ltd., Beijing 102206, China
| | - Zhan Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Caixia Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Wanlin Liu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Yuting Dong
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Sailong Ma
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- National Health Commission Key Laboratory of Respiratory Diseases, Tongji Hosptial, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qian Zhang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yiyun Zheng
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Liping Lou
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Dong Kuang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qian Chu
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jun Qin
- Beijing Pineal Diagnostics Co., Ltd., Beijing 102206, China
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Guoping Wang
- Institute of Pathology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- Department of Pathology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
- National Health Commission Key Laboratory of Respiratory Diseases, Tongji Hosptial, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yi Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| |
Collapse
|
4
|
Piersma SR, Valles-Marti A, Rolfs F, Pham TV, Henneman AA, Jiménez CR. Inferring kinase activity from phosphoproteomic data: Tool comparison and recent applications. MASS SPECTROMETRY REVIEWS 2024; 43:725-751. [PMID: 36156810 DOI: 10.1002/mas.21808] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Aberrant cellular signaling pathways are a hallmark of cancer and other diseases. One of the most important signaling mechanisms involves protein phosphorylation/dephosphorylation. Protein phosphorylation is catalyzed by protein kinases, and over 530 protein kinases have been identified in the human genome. Aberrant kinase activity is one of the drivers of tumorigenesis and cancer progression and results in altered phosphorylation abundance of downstream substrates. Upstream kinase activity can be inferred from the global collection of phosphorylated substrates. Mass spectrometry-based phosphoproteomic experiments nowadays routinely allow identification and quantitation of >10k phosphosites per biological sample. This substrate phosphorylation footprint can be used to infer upstream kinase activities using tools like Kinase Substrate Enrichment Analysis (KSEA), Posttranslational Modification Substrate Enrichment Analysis (PTM-SEA), and Integrative Inferred Kinase Activity Analysis (INKA). Since the topic of kinase activity inference is very active with many new approaches reported in the past 3 years, we would like to give an overview of the field. In this review, an inventory of kinase activity inference tools, their underlying algorithms, statistical frameworks, kinase-substrate databases, and user-friendliness is presented. The most widely-used tools are compared in-depth. Subsequently, recent applications of the tools are described focusing on clinical tissues and hematological samples. Two main application areas for kinase activity inference tools can be discerned. (1) Maximal biological insights can be obtained from large data sets with group comparisons using multiple complementary tools (e.g., PTM-SEA and KSEA or INKA). (2) In the oncology context where personalized treatment requires analysis of single samples, INKA for example, has emerged as tool that can prioritize actionable kinases for targeted inhibition.
Collapse
Affiliation(s)
- Sander R Piersma
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Andrea Valles-Marti
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Frank Rolfs
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Thang V Pham
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Alex A Henneman
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Connie R Jiménez
- OncoProteomics Laboratory Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| |
Collapse
|
5
|
Lai Q, Wan Y, Zhang Y, Huang Y, Tang Q, Chen M, Li Q, Ma K, Xiao P, Luo C, Zhuang X. Hypomethylation-associated LINC00987 downregulation induced lung adenocarcinoma progression by inhibiting the phosphorylation-mediated degradation of SND1. Mol Carcinog 2024; 63:1260-1274. [PMID: 38607240 DOI: 10.1002/mc.23722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/27/2024] [Accepted: 03/25/2024] [Indexed: 04/13/2024]
Abstract
DNA methylation, an epigenetic regulatory mechanism dictating gene transcription, plays a critical role in the occurrence and development of cancer. However, the molecular underpinnings of LINC00987 methylation in the regulation of lung adenocarcinoma (LUAD) remain elusive. This study investigated LINC00987 expression in LUAD patients through analysis of The Cancer Genome Atlas data sets. Quantitative real-time polymerase chain reaction (RT-qPCR) and fluorescence in situ hybridization assays were used to assess LINC00987 expression in LUAD. The bisulfite genomic sequence PCR (BSP) assay was used to determine the methylation levels of the LINC00987 promoter. The interaction between LINC00987 and SND1 was elucidated via immunoprecipitation and RNA pull-down assays. The functional significance of LINC00987 and SND1 in Calu-3 and NCI-H1688 cells was evaluated in vitro through CCK-8, EdU, Transwell, flow cytometry, and vasculogenic mimicry (VM) tube formation assays. LINC00987 expression decreased in LUAD concomitant with hypermethylation of the promoter region, while hypomethylation of the LINC00987 promoter in LUAD tissues correlated with tumor progression. Treatment with 5-Aza-CdR augmented LINC00987 expression and inhibited tumor growth. Mechanistically, LINC00987 overexpression impeded LUAD progression and VM through direct binding with SND1, thereby facilitating its phosphorylation and subsequent degradation. Additionally, overexpression of SND1 counteracted the adverse effects of LINC00987 downregulation on cell proliferation, apoptosis, cell migration, invasion, and VM in LUAD in vitro. In conclusion, this pioneering study focuses on the expression and function of LINC00987 and reveals that hypermethylation of the LINC00987 gene may contribute to LUAD progression. LINC00987 has emerged as a potential tumor suppressor gene in tumorigenesis through its binding with SND1 to facilitate its phosphorylation and subsequent degradation.
Collapse
Affiliation(s)
- Qi Lai
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yulin Wan
- Medical Department, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yingqian Zhang
- Laboratory of Nonhuman Primate Disease Modeling Research, West China Hospital, Sichuan University, Chengdu, China
| | - Yingzhao Huang
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Qiuyue Tang
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Mei Chen
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Qian Li
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Ke Ma
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Ping Xiao
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Cheng Luo
- Department of Radiation Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Xiang Zhuang
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|
6
|
Ramberger E, Sapozhnikova V, Ng YLD, Dolnik A, Ziehm M, Popp O, Sträng E, Kull M, Grünschläger F, Krüger J, Benary M, Müller S, Gao X, Murgai A, Haji M, Schmidt A, Lutz R, Nogai A, Braune J, Laue D, Langer C, Khandanpour C, Bassermann F, Döhner H, Engelhardt M, Straka C, Hundemer M, Beule D, Haas S, Keller U, Einsele H, Bullinger L, Knop S, Mertins P, Krönke J. The proteogenomic landscape of multiple myeloma reveals insights into disease biology and therapeutic opportunities. NATURE CANCER 2024:10.1038/s43018-024-00784-3. [PMID: 38942927 DOI: 10.1038/s43018-024-00784-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 05/15/2024] [Indexed: 06/30/2024]
Abstract
Multiple myeloma (MM) is a plasma cell malignancy of the bone marrow. Despite therapeutic advances, MM remains incurable, and better risk stratification as well as new therapies are therefore highly needed. The proteome of MM has not been systematically assessed before and holds the potential to uncover insight into disease biology and improved prognostication in addition to genetic and transcriptomic studies. Here we provide a comprehensive multiomics analysis including deep tandem mass tag-based quantitative global (phospho)proteomics, RNA sequencing, and nanopore DNA sequencing of 138 primary patient-derived plasma cell malignancies encompassing treatment-naive MM, plasma cell leukemia and the premalignancy monoclonal gammopathy of undetermined significance, as well as healthy controls. We found that the (phospho)proteome of malignant plasma cells are highly deregulated as compared with healthy plasma cells and is both defined by chromosomal alterations as well as posttranscriptional regulation. A prognostic protein signature was identified that is associated with aggressive disease independent of established risk factors in MM. Integration with functional genetics and single-cell RNA sequencing revealed general and genetic subtype-specific deregulated proteins and pathways in plasma cell malignancies that include potential targets for (immuno)therapies. Our study demonstrates the potential of proteogenomics in cancer and provides an easily accessible resource for investigating protein regulation and new therapeutic approaches in MM.
Collapse
Affiliation(s)
- Evelyn Ramberger
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Valeriia Sapozhnikova
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Yuen Lam Dora Ng
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Anna Dolnik
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Matthias Ziehm
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Oliver Popp
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Eric Sträng
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Miriam Kull
- Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Florian Grünschläger
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Josefine Krüger
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Sina Müller
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Xiang Gao
- Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | - Arunima Murgai
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Mohamed Haji
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
| | - Annika Schmidt
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Raphael Lutz
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | - Axel Nogai
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Jan Braune
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | - Dominik Laue
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
| | | | - Cyrus Khandanpour
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, Muenster, Germany
| | - Florian Bassermann
- Department of Medicine III, Technical University of Munich, Klinikum rechts der Isar, Munich, Germany
| | - Hartmut Döhner
- Internal Medicine III, University Hospital Ulm, Ulm, Germany
| | | | | | - Michael Hundemer
- Department of Medicine V, Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Heidelberg, Germany
| | | | - Simon Haas
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
- Berlin Institute of Health, Berlin, Germany
- German Cancer Research Center (DKFZ), Heidelberg, Germany
- Heidelberg Institute for Stem Cell Technology and Experimental Medicine, Heidelberg, Germany
| | - Ulrich Keller
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- Max Delbrück Center for Molecular Medicine, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | - Lars Bullinger
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Stefan Knop
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany.
- Nuremberg General Hospital, Nuremberg, Germany.
- Paracelsus Medical School, Nuremberg, Germany.
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.
- Berlin Institute of Health, Berlin, Germany.
| | - Jan Krönke
- Charité - Universitätsmedizin Berlin, Corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Berlin, Germany.
- German Cancer Consortium (DKTK), partner site Berlin, DKFZ and Charité - Universitätsmedizin Berlin, Berlin, Germany.
| |
Collapse
|
7
|
Whiteaker JR, Zhao L, Schoenherr RM, Huang D, Kennedy JJ, Ivey RG, Lin C, Lorentzen TD, Colantonio S, Caceres TW, Roberts RR, Knotts JG, Reading JJ, Perry CD, Garcia-Buntley SS, Bocik W, Hewitt SM, Paulovich AG. Characterization of an expanded set of assays for immunomodulatory proteins using targeted mass spectrometry. Sci Data 2024; 11:682. [PMID: 38918394 PMCID: PMC11199596 DOI: 10.1038/s41597-024-03467-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Accepted: 06/03/2024] [Indexed: 06/27/2024] Open
Abstract
Immunotherapies are revolutionizing cancer care, but many patients do not achieve durable responses and immune-related adverse events are difficult to predict. Quantifying the hundreds of proteins involved in cancer immunity has the potential to provide biomarkers to monitor and predict tumor response. We previously developed robust, multiplexed quantitative assays for immunomodulatory proteins using targeted mass spectrometry, providing measurements that can be performed reproducibly and harmonized across laboratories. Here, we expand upon those efforts in presenting data from a multiplexed immuno-oncology (IO)-3 assay panel targeting 43 peptides representing 39 immune- and inflammation-related proteins. A suite of novel monoclonal antibodies was generated as assay reagents, and the fully characterized antibodies are made available as a resource to the community. The publicly available dataset contains complete characterization of the assay performance, as well as the mass spectrometer parameters and reagent information necessary for implementation of the assay. Quantification of the proteins will provide benefit to correlative studies in clinical trials, identification of new biomarkers, and improve understanding of the immune response in cancer.
Collapse
Affiliation(s)
- Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Lei Zhao
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Regine M Schoenherr
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Dongqing Huang
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Chenwei Lin
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Travis D Lorentzen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Simona Colantonio
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Tessa W Caceres
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Rhonda R Roberts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joseph G Knotts
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Joshua J Reading
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Candice D Perry
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Sandra S Garcia-Buntley
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - William Bocik
- Cancer Research Technology Program, Antibody Characterization Lab, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Stephen M Hewitt
- Experimental Pathology Laboratory, Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| |
Collapse
|
8
|
Zhang C, Yang L, Zhao W, Zhu H, Shi S, Chen S, Wang G, Li B, Zhao G. A heterogeneous tumor immune microenvironment of uncommon epidermal growth factor receptor mutant non-small cell lung cancer. Cancer Sci 2024. [PMID: 38890815 DOI: 10.1111/cas.16253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 05/31/2024] [Accepted: 06/05/2024] [Indexed: 06/20/2024] Open
Abstract
Common epidermal growth factor receptor (EGFR) mutations are usually not considered for immunotherapy in non-small cell lung cancer (NSCLC) due to poor efficacy. However, whether uncommon EGFR mutations are suitable for immunotherapy has not been thoroughly studied. Thus, we explored the tumor immune microenvironment (TME) features in uncommon EGFR mutant NSCLC. In this study, a total of 41 patients with EGFR mutations were included, the majority (85.4%) of whom were stage I. Among them, 22 patients harbored common mutations, while 19 patients presented with uncommon mutations. Compared with common mutations, uncommon mutations exhibited more infiltrating T cells and fewer M2 macrophages, upregulated expression of antigen processing and a presentation pathway. Unsupervised clustering based on the mIF profile identified two classes with heterogeneous TME in uncommon mutations. Class 1 featured the absence of PD-1+ cytotoxic T cell infiltration, and class 2 displayed a hotter TME because of the downregulated expression of hypoxia (p < 0.001), oxidative phosphorylation (p = 0.009), and transforming growth factor beta signaling (p = 0.01) pathways as well as increased expression of CTLA4 (p = 0.001) and PDCD1 (p = 0.004). The association of CTLA4 and PDCD1 with TME profiles was validated in a TCGA lung adenocarcinoma cohort with uncommon EGFR mutations. Our study reveals the distinct and heterogeneous TME features in uncommon EGFR mutant NSCLC.
Collapse
Affiliation(s)
- Chong Zhang
- Health Science Center, Ningbo University, Ningbo, China
- Department of Thoracic Surgery, Ningbo No.2 Hospital, Ningbo, China
| | - Liangwei Yang
- Department of Thoracic Surgery, Ningbo No.2 Hospital, Ningbo, China
| | - Weidi Zhao
- Department of Thoracic Surgery, Ningbo No.2 Hospital, Ningbo, China
| | - Huangkai Zhu
- Department of Thoracic Surgery, Ningbo No.2 Hospital, Ningbo, China
| | - Shuo Shi
- Burning Rock Biotech, Guangzhou, China
| | | | | | - Bing Li
- Burning Rock Biotech, Guangzhou, China
| | - Guofang Zhao
- Health Science Center, Ningbo University, Ningbo, China
- Department of Thoracic Surgery, Ningbo No.2 Hospital, Ningbo, China
| |
Collapse
|
9
|
Wang J, Song X, Wei M, Qin L, Zhu Q, Wang S, Liang T, Hu W, Zhu X, Li J. PCAS: An Integrated Tool for Multi-Dimensional Cancer Research Utilizing Clinical Proteomic Tumor Analysis Consortium Data. Int J Mol Sci 2024; 25:6690. [PMID: 38928396 PMCID: PMC11203781 DOI: 10.3390/ijms25126690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/13/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
Proteomics offers a robust method for quantifying proteins and elucidating their roles in cellular functions, surpassing the insights provided by transcriptomics. The Clinical Proteomic Tumor Analysis Consortium database, enriched with comprehensive cancer proteomics data including phosphorylation and ubiquitination profiles, alongside transcriptomics data from the Genomic Data Commons, allow for integrative molecular studies of cancer. The ProteoCancer Analysis Suite (PCAS), our newly developed R package and Shinyapp, leverages these resources to facilitate in-depth analyses of proteomics, phosphoproteomics, and transcriptomics, enhancing our understanding of the tumor microenvironment through features like immune infiltration and drug sensitivity analysis. This tool aids in identifying critical signaling pathways and therapeutic targets, particularly through its detailed phosphoproteomic analysis. To demonstrate the functionality of the PCAS, we conducted an analysis of GAPDH across multiple cancer types, revealing a significant upregulation of protein levels, which is consistent with its important biological and clinical significance in tumors, as indicated in our prior research. Further experiments were used to validate the findings performed using the tool. In conclusion, the PCAS is a powerful and valuable tool for conducting comprehensive proteomic analyses, significantly enhancing our ability to uncover oncogenic mechanisms and identify potential therapeutic targets in cancer research.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Jianxiang Li
- School of Public Health, Suzhou Medical College of Soochow University, Suzhou 215123, China; (J.W.); (X.S.); (M.W.); (L.Q.); (Q.Z.); (S.W.); (T.L.); (W.H.); (X.Z.)
| |
Collapse
|
10
|
Yang Q, Yan C, Sun Y, Xie Z, Yang L, Jiang M, Ni J, Chen B, Xu S, Yuan Z, Wu Y, Liu X, Yuan Z, Bai Z. Extracellular Matrix Remodeling Alleviates Memory Deficits in Alzheimer's Disease by Enhancing the Astrocytic Autophagy-Lysosome Pathway. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2400480. [PMID: 38881515 DOI: 10.1002/advs.202400480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/21/2024] [Indexed: 06/18/2024]
Abstract
Extracellular matrix (ECM) remodeling is strongly linked to Alzheimer's disease (AD) risk; however, the underlying mechanisms are not fully understood. Here, it is found that the injection of chondroitinase ABC (ChABC), mimicking ECM remodeling, into the medial prefrontal cortex (mPFC) reversed short-term memory loss and reduced amyloid-beta (Aβ) deposition in 5xFAD mice. ECM remodeling also reactivated astrocytes, reduced the levels of aggrecan in Aβ plaques, and enhanced astrocyte recruitment to surrounding plaques. Importantly, ECM remodeling enhanced the autophagy-lysosome pathway in astrocytes, thereby mediating Aβ clearance and alleviating AD pathology. ECM remodeling also promoted Aβ plaque phagocytosis by astrocytes by activating the astrocytic phagocytosis receptor MERTK and promoting astrocytic vesicle circulation. The study identified a cellular mechanism in which ECM remodeling activates the astrocytic autophagy-lysosomal pathway and alleviates AD pathology. Targeting ECM remodeling may represent a potential therapeutic strategy for AD and serve as a reference for the treatment of this disease.
Collapse
Affiliation(s)
- Qinghu Yang
- School of Life Science & Research Center for Natural Peptide Drugs, Shaanxi Engineering & Technological Research Centre for Conservation & Utilization of Regional Biological Resources, Yanan University, Yanan, 716000, China
- Yanan Engineering & Technological Research Centre for Resource Peptide Drugs, Yanan Key Laboratory for Neural Immuno-Tumor and Stem Cell, Yanan, 716000, China
- The Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Chengxiang Yan
- School of Life Science & Research Center for Natural Peptide Drugs, Shaanxi Engineering & Technological Research Centre for Conservation & Utilization of Regional Biological Resources, Yanan University, Yanan, 716000, China
- Yanan Engineering & Technological Research Centre for Resource Peptide Drugs, Yanan Key Laboratory for Neural Immuno-Tumor and Stem Cell, Yanan, 716000, China
| | - Yahan Sun
- School of Life Science & Research Center for Natural Peptide Drugs, Shaanxi Engineering & Technological Research Centre for Conservation & Utilization of Regional Biological Resources, Yanan University, Yanan, 716000, China
- Yanan Engineering & Technological Research Centre for Resource Peptide Drugs, Yanan Key Laboratory for Neural Immuno-Tumor and Stem Cell, Yanan, 716000, China
| | - Zhen Xie
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Liang Yang
- School of Life Science & Research Center for Natural Peptide Drugs, Shaanxi Engineering & Technological Research Centre for Conservation & Utilization of Regional Biological Resources, Yanan University, Yanan, 716000, China
- Yanan Engineering & Technological Research Centre for Resource Peptide Drugs, Yanan Key Laboratory for Neural Immuno-Tumor and Stem Cell, Yanan, 716000, China
| | - Ming Jiang
- School of Life Science & Research Center for Natural Peptide Drugs, Shaanxi Engineering & Technological Research Centre for Conservation & Utilization of Regional Biological Resources, Yanan University, Yanan, 716000, China
- Yanan Engineering & Technological Research Centre for Resource Peptide Drugs, Yanan Key Laboratory for Neural Immuno-Tumor and Stem Cell, Yanan, 716000, China
| | - Junjun Ni
- Key Laboratory of Molecular Medicine and Biotherapy, Department of Biology, School of Life Science, Beijing Institute of Technology, Beijing, 100081, China
| | - Beining Chen
- The Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
- State Key Laboratory of Reproductive Medicine, Key Laboratory of Human Functional Genomics of Jiangsu Province, Department of Neurobiology, Interdisciplinary InnoCenter for Organoids, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, 211166, China
| | - Sen Xu
- School of Life Science & Research Center for Natural Peptide Drugs, Shaanxi Engineering & Technological Research Centre for Conservation & Utilization of Regional Biological Resources, Yanan University, Yanan, 716000, China
- Yanan Engineering & Technological Research Centre for Resource Peptide Drugs, Yanan Key Laboratory for Neural Immuno-Tumor and Stem Cell, Yanan, 716000, China
| | - Zhaoyue Yuan
- School of Life Science & Research Center for Natural Peptide Drugs, Shaanxi Engineering & Technological Research Centre for Conservation & Utilization of Regional Biological Resources, Yanan University, Yanan, 716000, China
- Yanan Engineering & Technological Research Centre for Resource Peptide Drugs, Yanan Key Laboratory for Neural Immuno-Tumor and Stem Cell, Yanan, 716000, China
| | - Yanyan Wu
- School of Life Science & Research Center for Natural Peptide Drugs, Shaanxi Engineering & Technological Research Centre for Conservation & Utilization of Regional Biological Resources, Yanan University, Yanan, 716000, China
- Yanan Engineering & Technological Research Centre for Resource Peptide Drugs, Yanan Key Laboratory for Neural Immuno-Tumor and Stem Cell, Yanan, 716000, China
| | - Xia Liu
- School of Life Science & Research Center for Natural Peptide Drugs, Shaanxi Engineering & Technological Research Centre for Conservation & Utilization of Regional Biological Resources, Yanan University, Yanan, 716000, China
- Yanan Engineering & Technological Research Centre for Resource Peptide Drugs, Yanan Key Laboratory for Neural Immuno-Tumor and Stem Cell, Yanan, 716000, China
| | - Zengqiang Yuan
- The Brain Science Center, Beijing Institute of Basic Medical Sciences, Beijing, 100850, China
| | - Zhantao Bai
- School of Life Science & Research Center for Natural Peptide Drugs, Shaanxi Engineering & Technological Research Centre for Conservation & Utilization of Regional Biological Resources, Yanan University, Yanan, 716000, China
- Yanan Engineering & Technological Research Centre for Resource Peptide Drugs, Yanan Key Laboratory for Neural Immuno-Tumor and Stem Cell, Yanan, 716000, China
| |
Collapse
|
11
|
Du P, Fan R, Zhang N, Wu C, Zhang Y. Advances in Integrated Multi-omics Analysis for Drug-Target Identification. Biomolecules 2024; 14:692. [PMID: 38927095 PMCID: PMC11201992 DOI: 10.3390/biom14060692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 06/08/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
As an essential component of modern drug discovery, the role of drug-target identification is growing increasingly prominent. Additionally, single-omics technologies have been widely utilized in the process of discovering drug targets. However, it is difficult for any single-omics level to clearly expound the causal connection between drugs and how they give rise to the emergence of complex phenotypes. With the progress of large-scale sequencing and the development of high-throughput technologies, the tendency in drug-target identification has shifted towards integrated multi-omics techniques, gradually replacing traditional single-omics techniques. Herein, this review centers on the recent advancements in the domain of integrated multi-omics techniques for target identification, highlights the common multi-omics analysis strategies, briefly summarizes the selection of multi-omics analysis tools, and explores the challenges of existing multi-omics analyses, as well as the applications of multi-omics technology in drug-target identification.
Collapse
Affiliation(s)
- Peiling Du
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Rui Fan
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Nana Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Chenyuan Wu
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| | - Yingqian Zhang
- School of Pharmacy, Hangzhou Normal University, Hangzhou 311121, China; (P.D.); (R.F.); (N.Z.); (C.W.)
- Key Laboratory of Elemene Class Anti-Cancer Chinese Medicines, Engineering Laboratory of Development and Application of Traditional Chinese Medicines, Collaborative Innovation Center of Traditional Chinese Medicines of Zhejiang Province, Hangzhou Normal University, Hangzhou 311121, China
| |
Collapse
|
12
|
Ru M, He J, Bai Y, Zhang K, Shi Q, Gao F, Wang Y, Li B, Shen L. Integration of Proteomic and Metabolomic Data Reveals the Lipid Metabolism Disorder in the Liver of Rats Exposed to Simulated Microgravity. Biomolecules 2024; 14:682. [PMID: 38927087 PMCID: PMC11201887 DOI: 10.3390/biom14060682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Long-term exposure to microgravity is considered to cause liver lipid accumulation, thereby increasing the risk of non-alcoholic fatty liver disease (NAFLD) among astronauts. However, the reasons for this persistence of symptoms remain insufficiently investigated. In this study, we used tandem mass tag (TMT)-based quantitative proteomics techniques, as well as non-targeted metabolomics techniques based on liquid chromatography-tandem mass spectrometry (LC-MS/MS), to comprehensively analyse the relative expression levels of proteins and the abundance of metabolites associated with lipid accumulation in rat liver tissues under simulated microgravity conditions. The differential analysis revealed 63 proteins and 150 metabolites between the simulated microgravity group and the control group. By integrating differentially expressed proteins and metabolites and performing pathway enrichment analysis, we revealed the dysregulation of major metabolic pathways under simulated microgravity conditions, including the biosynthesis of unsaturated fatty acids, linoleic acid metabolism, steroid hormone biosynthesis and butanoate metabolism, indicating disrupted liver metabolism in rats due to weightlessness. Finally, we examined differentially expressed proteins associated with lipid metabolism in the liver of rats exposed to stimulated microgravity. These findings contribute to identifying the key molecules affected by microgravity and could guide the design of rational nutritional or pharmacological countermeasures for astronauts.
Collapse
Affiliation(s)
- Mengyao Ru
- School of Basic Medicine, Yan’an University, Yan’an 716000, China; (M.R.); (K.Z.)
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi’an 710032, China;
| | - Jun He
- Department of Anesthesiology, Xi’an No.3 Hospital, The Affiliated Hospital of Northwest University, Xi’an 710018, China;
| | - Yungang Bai
- Department of Aerospace Medicine, The Fourth Military Medical University, Xi’an 710032, China; (Y.B.); (Y.W.)
| | - Kun Zhang
- School of Basic Medicine, Yan’an University, Yan’an 716000, China; (M.R.); (K.Z.)
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi’an 710032, China;
| | - Qianqian Shi
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi’an 710032, China;
- School of Life Sciences, Yan’an University, Yan’an 716000, China
| | - Fang Gao
- Department of Neurobiology, The Fourth Military Medical University, Xi’an 710032, China;
| | - Yunying Wang
- Department of Aerospace Medicine, The Fourth Military Medical University, Xi’an 710032, China; (Y.B.); (Y.W.)
| | - Baoli Li
- Yan’an Key Laboratory of Microbial Drug Innovation and Transformation, Yan’an University, Yan’an 716000, China
| | - Lan Shen
- The State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, The Fourth Military Medical University, Xi’an 710032, China;
| |
Collapse
|
13
|
Liu Z, Lu Q, Zhang Z, Feng Q, Wang X. TMPRSS2 is a tumor suppressor and its downregulation promotes antitumor immunity and immunotherapy response in lung adenocarcinoma. Respir Res 2024; 25:238. [PMID: 38862975 PMCID: PMC11167788 DOI: 10.1186/s12931-024-02870-7] [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: 10/07/2023] [Accepted: 06/06/2024] [Indexed: 06/13/2024] Open
Abstract
BACKGROUND TMPRSS2, a key molecule for SARS-CoV-2 invading human host cells, has an association with cancer. However, its association with lung cancer remains insufficiently unexplored. METHODS In five bulk transcriptomics datasets, one single-cell RNA sequencing (scRNA-seq) dataset and one proteomics dataset for lung adenocarcinoma (LUAD), we explored associations between TMPRSS2 expression and immune signatures, tumor progression phenotypes, genomic features, and clinical prognosis in LUAD by the bioinformatics approach. Furthermore, we performed experimental validation of the bioinformatics findings. RESULTS TMPRSS2 expression levels correlated negatively with the enrichment levels of both immune-stimulatory and immune-inhibitory signatures, while they correlated positively with the ratios of immune-stimulatory/immune-inhibitory signatures. It indicated that TMPRSS2 levels had a stronger negative correlation with immune-inhibitory than with immune-stimulatory signatures. TMPRSS2 downregulation correlated with increased proliferation, stemness, genomic instability, tumor progression, and worse survival in LUAD. We further validated that TMPRSS2 was downregulated with tumor progression in the LUAD cohort we collected from Jiangsu Cancer Hospital, China. In vitro and in vivo experiments verified the association of TMPRSS2 deficiency with increased tumor cell proliferation and invasion and antitumor immunity in LUAD. Moreover, in vivo experiments demonstrated that TMPRSS2-knockdown tumors were more sensitive to BMS-1, an inhibitor of PD-1/PD-L1. CONCLUSIONS TMPRSS2 is a tumor suppressor, while its downregulation is a positive biomarker of immunotherapy in LUAD. Our data provide a potential link between lung cancer and pneumonia caused by SARS-CoV-2 infection.
Collapse
Affiliation(s)
- Zhixian Liu
- Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, 210009, China
| | - Qiqi Lu
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China
| | - Zhilan Zhang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China
| | - Qiushi Feng
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
- Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, 211198, China.
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China.
| |
Collapse
|
14
|
Thiery J, Fahrner M. Integration of proteomics in the molecular tumor board. Proteomics 2024; 24:e2300002. [PMID: 38143279 DOI: 10.1002/pmic.202300002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Revised: 12/03/2023] [Accepted: 12/05/2023] [Indexed: 12/26/2023]
Abstract
Cancer remains one of the most complex and challenging diseases in mankind. To address the need for a personalized treatment approach for particularly complex tumor cases, molecular tumor boards (MTBs) have been initiated. MTBs are interdisciplinary teams that perform in-depth molecular diagnostics to cooperatively and interdisciplinarily advise on the best therapeutic strategy. Current molecular diagnostics are routinely performed on the transcriptomic and genomic levels, aiming to identify tumor-driving mutations. However, these approaches can only partially capture the actual phenotype and the molecular key players of tumor growth and progression. Thus, direct investigation of the expressed proteins and activated signaling pathways provide valuable complementary information on the tumor-driving molecular characteristics of the tissue. Technological advancements in mass spectrometry-based proteomics enable the robust, rapid, and sensitive detection of thousands of proteins in minimal sample amounts, paving the way for clinical proteomics and the probing of oncogenic signaling activity. Therefore, proteomics is currently being integrated into molecular diagnostics within MTBs and holds promising potential in aiding tumor classification and identifying personalized treatment strategies. This review introduces MTBs and describes current clinical proteomics, its potential in precision oncology, and highlights the benefits of multi-omic data integration.
Collapse
Affiliation(s)
- Johanna Thiery
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Matthias Fahrner
- Institute for Surgical Pathology, Medical Center - University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
- German Cancer Consortium (DKTK) and Cancer Research Center (DKFZ), Freiburg, Germany
| |
Collapse
|
15
|
Li X, Gu Y, Hu B, Shao M, Li H. A liquid biopsy assay for the noninvasive detection of lymph node metastases in T1 lung adenocarcinoma. Thorac Cancer 2024; 15:1312-1319. [PMID: 38682829 PMCID: PMC11147666 DOI: 10.1111/1759-7714.15315] [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: 03/05/2024] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 05/01/2024] Open
Abstract
INTRODUCTION Lung adenocarcinoma (LUAD) is a common pathological type of lung cancer. The presence of lymph node metastasis plays a crucial role in determining the overall treatment approach and long-term prognosis for early LUAD, therefore accurate prediction of lymph node metastasis is essential to guide treatment decisions and ultimately improve patient outcomes. METHODS We performed transcriptome sequencing on T1 LUAD patients with positive or negative lymph node metastases and combined this data with The Cancer Genome Atlas Program cohort to identify potential risk molecules at the tissue level. Subsequently, by detecting the expression of these risk molecules by real-time quantitative PCR in serum samples, we developed a model to predict the risk of lymph node metastasis from a training cohort of 96 patients and a validation cohort of 158 patients. RESULTS Through transcriptome sequencing analysis of tissue samples, we identified 11 RNA (miR-412, miR-219, miR-371, FOXC1, ID1, MMP13, COL11A1, PODXL2, CXCL13, SPOCK1 and MECOM) associated with positive lymph node metastases in T1 LUAD. As the expression of FOXC1 and COL11A1 was not detected in serum, we constructed a predictive model that accurately identifies patients with positive lymph node metastases using the remaining nine RNA molecules in the serum of T1 LUAD patients. In the training set, the model achieved an area under the curve (AUC) of 0.89, and in the validation set, the AUC was 0.91. CONCLUSIONS We have established a new risk prediction model using serum samples from T1 LUAD patients, enabling noninvasive identification of those with positive lymph node metastases.
Collapse
Affiliation(s)
- Xin Li
- Department of Thoracic Surgery, Beijing Institute of Respiratory Medicine and Beijing Chao‐Yang HospitalCapital Medical UniversityBeijingChina
| | - Yang Gu
- Department of Thoracic Surgery, Beijing Institute of Respiratory Medicine and Beijing Chao‐Yang HospitalCapital Medical UniversityBeijingChina
| | - Bin Hu
- Department of Thoracic Surgery, Beijing Institute of Respiratory Medicine and Beijing Chao‐Yang HospitalCapital Medical UniversityBeijingChina
| | - Ming‐Ming Shao
- Department of Respiratory and Critical Care Medicine, Beijing Institute of Respiratory Medicine and Beijing Chao‐Yang HospitalCapital Medical UniversityBeijingChina
| | - Hui Li
- Department of Thoracic Surgery, Beijing Institute of Respiratory Medicine and Beijing Chao‐Yang HospitalCapital Medical UniversityBeijingChina
| |
Collapse
|
16
|
Zhou Z, Lin T, Chen S, Zhang G, Xu Y, Zou H, Zhou A, Zhang Y, Weng S, Han X, Liu Z. Omics-based molecular classifications empowering in precision oncology. Cell Oncol (Dordr) 2024; 47:759-777. [PMID: 38294647 DOI: 10.1007/s13402-023-00912-8] [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] [Accepted: 12/23/2023] [Indexed: 02/01/2024] Open
Abstract
BACKGROUND In the past decades, cancer enigmatical heterogeneity at distinct expression levels could interpret disparities in therapeutic response and prognosis. It built hindrances to precision medicine, a tactic to tailor customized treatment informed by the tumors' molecular profile. Single-omics analysis dissected the biological features associated with carcinogenesis to some extent but still failed to revolutionize cancer treatment as expected. Integrated omics analysis incorporated tumor biological networks from diverse layers and deciphered a holistic overview of cancer behaviors, yielding precise molecular classification to facilitate the evolution and refinement of precision medicine. CONCLUSION This review outlined the biomarkers at multiple expression layers to tutor molecular classification and pinpoint tumor diagnosis, and explored the paradigm shift in precision therapy: from single- to multi-omics-based subtyping to optimize therapeutic regimens. Ultimately, we firmly believe that by parsing molecular characteristics, omics-based typing will be a powerful assistant for precision oncology.
Collapse
Affiliation(s)
- Zhaokai Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Ting Lin
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Shuang Chen
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Yudi Xu
- Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Haijiao Zou
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Aoyang Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan, 450052, China.
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan, 450052, China.
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan, 450052, China.
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, China.
| |
Collapse
|
17
|
Wang Y, Yuan R, Liang B, Zhang J, Wen Q, Chen H, Tian Y, Wen L, Zhou H. A "One-Step" Strategy for the Global Characterization of Core-Fucosylated Glycoproteome. JACS AU 2024; 4:2005-2018. [PMID: 38818065 PMCID: PMC11134376 DOI: 10.1021/jacsau.4c00214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 04/21/2024] [Accepted: 04/22/2024] [Indexed: 06/01/2024]
Abstract
Core fucosylation, a special type of N-linked glycosylation, is important in tumor proliferation, invasion, metastatic potential, and therapy resistance. However, the core-fucosylated glycoproteome has not been extensively profiled due to the low abundance and poor ionization efficiency of glycosylated peptides. Here, a "one-step" strategy has been described for protein core-fucosylation characterization in biological samples. Core-fucosylated peptides can be selectively labeled with a glycosylated probe, which is linked with a temperature-sensitive poly(N-isopropylacrylamide) (PNIPAM) polymer, by mutant endoglycosidase (EndoF3-D165A). The labeled probe can be further removed by wild-type endoglycosidase (EndoF3) in a traceless manner for mass spectrometry (MS) analysis. The feasibility and effectiveness of the "one-step" strategy are evaluated in bovine serum albumin (BSA) spiked with standard core-fucosylated peptides, H1299, and Jurkat cell lines. The "one-step" strategy is then employed to characterize core-fucosylated sites in human lung adenocarcinoma, resulting in the identification of 2494 core-fucosylated sites distributed on 1176 glycoproteins. Further data analysis reveals that 196 core-fucosylated sites are significantly upregulated in tumors, which may serve as potential drug development targets or diagnostic biomarkers. Together, this "one-step" strategy has great potential for use in global and in-depth analysis of the core-fucosylated glycoproteome to promote its mechanism research.
Collapse
Affiliation(s)
- Yuqiu Wang
- Department
of Otolaryngology, Eye & ENT Hospital, Fudan University, Shanghai 200031, China
- Department
of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy
of Sciences, Shanghai 201203, China
| | - Rui Yuan
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, China
| | - Bo Liang
- Department
of Hematology, Xinxiang Central Hospital, Xinxiang 453000, China
| | - Jing Zhang
- Department
of Thoracic Surgery, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai 200433, China
| | - Qin Wen
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, China
| | - Hongxu Chen
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, China
| | - Yinping Tian
- Carbohydrate-Based
Drug Research Center, State Key Laboratory of Chemical Biology, Shanghai
Institute of Materia Medica, Chinese Academy
of Sciences, Shanghai 201203, China
| | - Liuqing Wen
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, China
- Carbohydrate-Based
Drug Research Center, State Key Laboratory of Chemical Biology, Shanghai
Institute of Materia Medica, Chinese Academy
of Sciences, Shanghai 201203, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
| | - Hu Zhou
- Department
of Analytical Chemistry, State Key Laboratory of Drug Research, Shanghai
Institute of Materia Medica, Chinese Academy
of Sciences, Shanghai 201203, China
- School
of Chinese Materia Medica, Nanjing University
of Chinese Medicine, Nanjing 210023, China
- University
of Chinese Academy of Sciences, Beijing 100049, China
- School
of Pharmaceutical Science and Technology, Hangzhou Institute for Advanced
Study, University of Chinese Academy of
Sciences, Hangzhou 310024, China
| |
Collapse
|
18
|
Bai Y, Li J, Wei Y, Chen Z, Liu Z, Guo D, Jia X, Niu Y, Shi B, Zhang X, Zhao Z, Hu J, Han X, Wang J, Liu X, Li S. Proteome Analysis Related to Unsaturated Fatty Acid Synthesis by Interfering with Bovine Adipocyte ACSL1 Gene. Antioxidants (Basel) 2024; 13:641. [PMID: 38929080 PMCID: PMC11200461 DOI: 10.3390/antiox13060641] [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: 04/27/2024] [Revised: 05/21/2024] [Accepted: 05/22/2024] [Indexed: 06/28/2024] Open
Abstract
Unsaturated fatty acids (UFAs) in beef play a vital role in promoting human health. Long-chain fatty acyl-CoA synthase 1 (ACSL1) is a crucial gene for UFA synthesis in bovine adipocytes. To investigate the protein expression profile during UFA synthesis, we performed a proteomic analysis of bovine adipocytes by RNA interference and non-interference with ACSL1 using label-free techniques. A total of 3558 proteins were identified in both the NC and si-treated groups, of which 1428 were differentially expressed proteins (DEPs; fold change ≥ 1.2 or ≤ 0.83 and p-value < 0.05). The enrichment analysis of the DEPs revealed signaling pathways related to UFA synthesis or metabolism, including cAMP, oxytocin, fatty acid degradation, glycerol metabolism, insulin, and the regulation of lipolysis in adipocytes (p-value < 0.05). Furthermore, based on the enrichment analysis of the DEPs, we screened 50 DEPs that potentially influence the synthesis of UFAs and constructed an interaction network. Moreover, by integrating our previously published transcriptome data, this study established a regulatory network involving differentially expressed long non-coding RNAs (DELs), highlighting 21 DEPs and 13 DELs as key genes involved in UFA synthesis. These findings present potential candidate genes for further investigation into the molecular mechanisms underlying UFA synthesis in bovines, thereby offering insights to enhance the quality of beef and contribute to consumer health in future studies.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Zhidong Zhao
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.B.); (J.L.); (Y.W.); (Z.C.); (Z.L.); (D.G.); (X.J.); (Y.N.); (B.S.); (X.Z.); (X.H.); (J.W.); (X.L.); (S.L.)
| | - Jiang Hu
- Gansu Key Laboratory of Herbivorous Animal Biotechnology, College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (Y.B.); (J.L.); (Y.W.); (Z.C.); (Z.L.); (D.G.); (X.J.); (Y.N.); (B.S.); (X.Z.); (X.H.); (J.W.); (X.L.); (S.L.)
| | | | | | | | | |
Collapse
|
19
|
Novoloaca A, Broc C, Beloeil L, Yu WH, Becker J. Comparative analysis of integrative classification methods for multi-omics data. Brief Bioinform 2024; 25:bbae331. [PMID: 38985929 PMCID: PMC11234228 DOI: 10.1093/bib/bbae331] [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: 12/19/2023] [Revised: 05/31/2024] [Indexed: 07/12/2024] Open
Abstract
Recent advances in sequencing, mass spectrometry, and cytometry technologies have enabled researchers to collect multiple 'omics data types from a single sample. These large datasets have led to a growing consensus that a holistic approach is needed to identify new candidate biomarkers and unveil mechanisms underlying disease etiology, a key to precision medicine. While many reviews and benchmarks have been conducted on unsupervised approaches, their supervised counterparts have received less attention in the literature and no gold standard has emerged yet. In this work, we present a thorough comparison of a selection of six methods, representative of the main families of intermediate integrative approaches (matrix factorization, multiple kernel methods, ensemble learning, and graph-based methods). As non-integrative control, random forest was performed on concatenated and separated data types. Methods were evaluated for classification performance on both simulated and real-world datasets, the latter being carefully selected to cover different medical applications (infectious diseases, oncology, and vaccines) and data modalities. A total of 15 simulation scenarios were designed from the real-world datasets to explore a large and realistic parameter space (e.g. sample size, dimensionality, class imbalance, effect size). On real data, the method comparison showed that integrative approaches performed better or equally well than their non-integrative counterpart. By contrast, DIABLO and the four random forest alternatives outperform the others across the majority of simulation scenarios. The strengths and limitations of these methods are discussed in detail as well as guidelines for future applications.
Collapse
Affiliation(s)
- Alexei Novoloaca
- BIOASTER Research Institute, 40 avenue Tony Garnier, F-69007 Lyon, France
| | - Camilo Broc
- BIOASTER Research Institute, 40 avenue Tony Garnier, F-69007 Lyon, France
| | - Laurent Beloeil
- BIOASTER Research Institute, 40 avenue Tony Garnier, F-69007 Lyon, France
| | - Wen-Han Yu
- Bill & Melinda Gates Medical Research Institute, Cambridge, Massachusetts, MA 02139, United States
| | - Jérémie Becker
- BIOASTER Research Institute, 40 avenue Tony Garnier, F-69007 Lyon, France
| |
Collapse
|
20
|
Tam YB, Low K, Ps H, Chadha M, Burns J, Wilding CP, Arthur A, Chen TW, Thway K, Sadanandam A, Jones RL, Huang PH. Proteomic features of soft tissue tumours in adolescents and young adults. COMMUNICATIONS MEDICINE 2024; 4:93. [PMID: 38762630 PMCID: PMC11102500 DOI: 10.1038/s43856-024-00522-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 05/07/2024] [Indexed: 05/20/2024] Open
Abstract
BACKGROUND Adolescents and young adult (AYA) patients with soft tissue tumours including sarcomas are an underserved group with disparities in treatment outcomes. METHODS To define the molecular features between AYA and older adult (OA) patients, we analysed the proteomic profiles of a large cohort of soft tissue tumours across 10 histological subtypes (AYA n = 66, OA n = 243), and also analysed publicly available functional genomic data from soft tissue tumour cell lines (AYA n = 5, OA n = 8). RESULTS Biological hallmarks analysis demonstrates that OA tumours are significantly enriched in MYC targets compared to AYA tumours. By comparing the patient-level proteomic data with functional genomic profiles from sarcoma cell lines, we show that the mRNA splicing pathway is an intrinsic vulnerability in cell lines from OA patients and that components of the spliceosome complex are independent prognostic factors for metastasis free survival in AYA patients. CONCLUSIONS Our study highlights the importance of performing age-specific molecular profiling studies to identify risk stratification tools and targeted agents tailored for the clinical management of AYA patients.
Collapse
Affiliation(s)
- Yuen Bun Tam
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Kaan Low
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Hari Ps
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Madhumeeta Chadha
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Jessica Burns
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Christopher P Wilding
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Amani Arthur
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Tom W Chen
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
- Graduate Institute of Oncology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Khin Thway
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
| | - Anguraj Sadanandam
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom
| | - Robin L Jones
- The Royal Marsden NHS Foundation Trust, London, United Kingdom
- Division of Clinical Studies, The Institute of Cancer Research, London, United Kingdom
| | - Paul H Huang
- Division of Molecular Pathology, The Institute of Cancer Research, London, United Kingdom.
| |
Collapse
|
21
|
Zheng JM, Lou CX, Huang YL, Song WT, Luo YC, Mo GY, Tan LY, Chen SW, Li BJ. Associations between immune cell phenotypes and lung cancer subtypes: insights from mendelian randomization analysis. BMC Pulm Med 2024; 24:242. [PMID: 38755605 PMCID: PMC11100125 DOI: 10.1186/s12890-024-03059-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 05/10/2024] [Indexed: 05/18/2024] Open
Abstract
INTRODUCTION Lung cancer is a common malignant tumor, and different types of immune cells may have different effects on the occurrence and development of lung cancer subtypes, including lung squamous cell carcinoma (LUSC) and lung adenocarcinoma (LUAD). However, the causal relationship between immune phenotype and lung cancer is still unclear. METHODS This study utilized a comprehensive dataset containing 731 immune phenotypes from the European Bioinformatics Institute (EBI) to evaluate the potential causal relationship between immune phenotypes and LUSC and LUAD using the inverse variance weighted (IVW) method in Mendelian randomization (MR). Sensitivity analyses, including MR-Egger intercept, Cochran Q test, and others, were conducted for the robustness of the results. The study results were further validated through meta-analysis using data from the Transdisciplinary Research Into Cancer of the Lung (TRICL) data. Additionally, confounding factors were excluded to ensure the robustness of the findings. RESULTS Among the final selection of 729 immune cell phenotypes, three immune phenotypes exhibited statistically significant effects with LUSC. CD28 expression on resting CD4 regulatory T cells (OR 1.0980, 95% CI: 1.0627-1.1344, p < 0.0001) and CD45RA + CD28- CD8 + T cell %T cell (OR 1.0011, 95% CI: 1.0007; 1.0015, p < 0.0001) were associated with increased susceptibility to LUSC. Conversely, CCR2 expression on monocytes (OR 0.9399, 95% CI: 0.9177-0.9625, p < 0.0001) was correlated with a decreased risk of LUSC. However, no significant causal relationships were established between any immune cell phenotypes and LUAD. CONCLUSION This study demonstrates that specific immune cell types are associated with the risk of LUSC but not with LUAD. While these findings are derived solely from European populations, they still provide clues for a deeper understanding of the immunological mechanisms underlying lung cancer and may offer new directions for future therapeutic strategies and preventive measures.
Collapse
Affiliation(s)
- Jin-Min Zheng
- Department of Surgery, Guangxi Medical University, Nanning, Guangxi, China
| | - Chen-Xi Lou
- Department of Surgery, Guangxi University of Chinese Medicine, Nanning, Guangxi, China
| | - Yu-Liang Huang
- Department of Surgery, Guangxi Medical University, Nanning, Guangxi, China
| | - Wen-Tao Song
- Department of Surgery, Youjiang Medical University For Nationalities, Baise, Guangxi, China
| | - Yi-Chen Luo
- Department of thoracic surgery, Guangxi Academy of Medical Sciences and the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China
| | - Guan-Yong Mo
- Department of thoracic surgery, Guilin Medical University, Guilin, Guangxi, China
| | - Lin-Yuan Tan
- Department of Surgery, Guangxi Medical University, Nanning, Guangxi, China
| | - Shang-Wei Chen
- Department of thoracic surgery, Guangxi Academy of Medical Sciences and the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi, China.
| | - Bai-Jun Li
- Department of thoracic surgery, Tumor Hospital of Guangxi Medical University, Nanning, Guangxi, China.
| |
Collapse
|
22
|
Bagnyukova T, Egleston BL, Pavlov VA, Serebriiskii IG, Golemis EA, Borghaei H. Synergy of EGFR and AURKA Inhibitors in KRAS-mutated Non-small Cell Lung Cancers. CANCER RESEARCH COMMUNICATIONS 2024; 4:1227-1239. [PMID: 38639476 PMCID: PMC11078142 DOI: 10.1158/2767-9764.crc-23-0482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/29/2024] [Accepted: 04/16/2024] [Indexed: 04/20/2024]
Abstract
The most common oncogenic driver mutations for non-small cell lung cancer (NSCLC) activate EGFR or KRAS. Clinical trials exploring treatments for EGFR- or KRAS-mutated (EGFRmut or KRASmut) cancers have focused on small-molecule inhibitors targeting the driver mutations. Typically, these inhibitors perform more effectively based on combination with either chemotherapies, or other targeted therapies. For EGFRmut NSCLC, a combination of inhibitors of EGFR and Aurora-A kinase (AURKA), an oncogene commonly overexpressed in solid tumors, has shown promising activity in clinical trials. Interestingly, a number of recent studies have indicated that EGFR activity supports overall viability of tumors lacking EGFR mutations, and AURKA expression is abundant in KRASmut cell lines. In this study, we have evaluated dual inhibition of EGFR and AURKA in KRASmut NSCLC models. These data demonstrate synergy between the EGFR inhibitor erlotinib and the AURKA inhibitor alisertib in reducing cell viability and clonogenic capacity in vitro, associated with reduced activity of EGFR pathway effectors, accumulation of enhanced aneuploid cell populations, and elevated cell death. Importantly, the erlotinib-alisertib combination also synergistically reduces xenograft growth in vivo. Analysis of signaling pathways demonstrated that the combination of erlotinib and alisertib was more effective than single-agent treatments at reducing activity of EGFR and pathway effectors following either brief or extended administration of the drugs. In sum, this study indicates value of inhibiting EGFR in KRASmut NSCLC, and suggests the specific value of dual inhibition of AURKA and EGFR in these tumors. SIGNIFICANCE The introduction of specific KRAS G12C inhibitors to the clinical practice in lung cancer has opened up opportunities that did not exist before. However, G12C alterations are only a subtype of all KRAS mutations observed. Given the high expression of AURKA in KRASmut NSCLC, our study could point to a potential therapeutic option for this subgroup of patients.
Collapse
Affiliation(s)
- Tetyana Bagnyukova
- Program in Cell Signaling and Metastasis, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Brian L. Egleston
- Program in Cell Signaling and Metastasis, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Valerii A. Pavlov
- Program in Cell Signaling and Metastasis, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russian Federation
| | - Ilya G. Serebriiskii
- Program in Cell Signaling and Metastasis, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Kazan Federal University, Kazan, Russian Federation
| | - Erica A. Golemis
- Program in Cell Signaling and Metastasis, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine at Temple University, Philadelphia, Pennsylvania
| | - Hossein Borghaei
- Program in Cell Signaling and Metastasis, Fox Chase Cancer Center, Philadelphia, Pennsylvania
- Division of Thoracic Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| |
Collapse
|
23
|
Park SJ, Ju S, Goh SH, Yoon BH, Park JL, Kim JH, Lee S, Lee SJ, Kwon Y, Lee W, Park KC, Lee GK, Park SY, Kim S, Kim SY, Han JY, Lee C. Proteogenomic Characterization Reveals Estrogen Signaling as a Target for Never-Smoker Lung Adenocarcinoma Patients without EGFR or ALK Alterations. Cancer Res 2024; 84:1491-1503. [PMID: 38607364 DOI: 10.1158/0008-5472.can-23-1551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 10/24/2023] [Accepted: 01/18/2024] [Indexed: 04/13/2024]
Abstract
Never-smoker lung adenocarcinoma (NSLA) is prevalent in Asian populations, particularly in women. EGFR mutations and anaplastic lymphoma kinase (ALK) fusions are major genetic alterations observed in NSLA, and NSLA with these alterations have been well studied and can be treated with targeted therapies. To provide insights into the molecular profile of NSLA without EGFR and ALK alterations (NENA), we selected 141 NSLA tissues and performed proteogenomic characterization, including whole genome sequencing (WGS), transcriptomic, methylation EPIC array, total proteomic, and phosphoproteomic analyses. Forty patients with NSLA harboring EGFR and ALK alterations and seven patients with NENA with microsatellite instability were excluded. Genome analysis revealed that TP53 (25%), KRAS (22%), and SETD2 (11%) mutations and ROS1 fusions (14%) were the most frequent genetic alterations in NENA patients. Proteogenomic impact analysis revealed that STK11 and ERBB2 somatic mutations had broad effects on cancer-associated genes in NENA. DNA copy number alteration analysis identified 22 prognostic proteins that influenced transcriptomic and proteomic changes. Gene set enrichment analysis revealed estrogen signaling as the key pathway activated in NENA. Increased estrogen signaling was associated with proteogenomic alterations, such as copy number deletions in chromosomes 14 and 21, STK11 mutation, and DNA hypomethylation of LLGL2 and ST14. Finally, saracatinib, an Src inhibitor, was identified as a potential drug for targeting activated estrogen signaling in NENA and was experimentally validated in vitro. Collectively, this study enhanced our understanding of NENA NSLA by elucidating the proteogenomic landscape and proposed saracatinib as a potential treatment for this patient population that lacks effective targeted therapies. SIGNIFICANCE The proteogenomic landscape in never-smoker lung cancer without known driver mutations reveals prognostic proteins and enhanced estrogen signaling that can be targeted as a potential therapeutic strategy to improve patient outcomes.
Collapse
Affiliation(s)
- Seung-Jin Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | - Shinyeong Ju
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Sung-Ho Goh
- National Cancer Center, Goyang, Republic of Korea
| | - Byoung-Ha Yoon
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jong-Lyul Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Jeong-Hwan Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Seonjeong Lee
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seoul, Republic of Korea
| | - Sang-Jin Lee
- National Cancer Center, Goyang, Republic of Korea
| | - Yumi Kwon
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Wonyeop Lee
- National Cancer Center, Goyang, Republic of Korea
| | - Kyung Chan Park
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
| | | | | | - Sunshin Kim
- National Cancer Center, Goyang, Republic of Korea
| | - Seon-Young Kim
- Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
- Department of Bioscience, University of Science and Technology (UST), Daejeon, Republic of Korea
- Korea Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Ji-Youn Han
- National Cancer Center, Goyang, Republic of Korea
| | - Cheolju Lee
- Chemical and Biological Integrative Research Center, Korea Institute of Science and Technology, Seoul, Republic of Korea
- Division of Bio-Medical Science and Technology, KIST School, University of Science and Technology, Seoul, Republic of Korea
| |
Collapse
|
24
|
Tong M, Liu Z, Li J, Wei X, Shi W, Liang C, Yu C, Huang R, Lin Y, Wang X, Wang S, Wang Y, Huang J, Wang Y, Li T, Qin J, Zhan D, Ji ZL. PhosMap: An ensemble bioinformatic platform to empower interactive analysis of quantitative phosphoproteomics. Comput Biol Med 2024; 174:108391. [PMID: 38613887 DOI: 10.1016/j.compbiomed.2024.108391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 03/18/2024] [Accepted: 04/01/2024] [Indexed: 04/15/2024]
Abstract
BACKGROUND Liquid chromatography-mass spectrometry (LC-MS)-based quantitative phosphoproteomics has been widely used to detect thousands of protein phosphorylation modifications simultaneously from the biological specimens. However, the complicated procedures for analyzing phosphoproteomics data has become a bottleneck to widening its application. METHODS Here, we develop PhosMap, a versatile and scalable tool to accomplish phosphoproteomics data analysis. A standardized phosphorylation data format was created for data analyses, from data preprocessing to downstream bioinformatic analyses such as dimension reduction, differential phosphorylation analysis, kinase activity, survival analysis, and so on. For better usability, we distribute PhosMap as a Docker image for easy local deployment upon any of Windows, Linux, and Mac system. RESULTS The source code is deposited at https://github.com/BADD-XMU/PhosMap. A free PhosMap webserver (https://huggingface.co/spaces/Bio-Add/PhosMap), with easy-to-follow fashion of dashboards, is curated for interactive data analysis. CONCLUSIONS PhosMap fills the technical gap of large-scale phosphorylation research by empowering researchers to process their own phosphoproteomics data expediently and efficiently, and facilitates better data interpretation.
Collapse
Affiliation(s)
- Mengsha Tong
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Zan Liu
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Jiaao Li
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China
| | - Xin Wei
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Wenhao Shi
- Analysis Center, Chemistry Department, Tsinghua University, Beijing, 100084, China
| | - Chenyu Liang
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Chunyu Yu
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Rongting Huang
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China
| | - Yuxiang Lin
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Xinkang Wang
- National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Shun Wang
- Departments of Pathology, National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yi Wang
- Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Jialiang Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China
| | - Yini Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China
| | - Tingting Li
- Department of Biomedical Informatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, 100191, China.
| | - Jun Qin
- Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing, 102206, China.
| | - Dongdong Zhan
- Beijing Pineal Diagnostics Co., Ltd., Beijing, 102206, China.
| | - Zhi-Liang Ji
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, Fujian, 361102, China; National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, Fujian, 361102, China.
| |
Collapse
|
25
|
Lu YF, Chang YH, Chen YJ, Hsieh MS, Lin MW, Hsu HH, Han CL, Chen YJ, Yu SL, Chen JS, Chen HY. Proteomic profiling of tumor microenvironment and prognosis risk prediction in stage I lung adenocarcinoma. Lung Cancer 2024; 191:107791. [PMID: 38621342 DOI: 10.1016/j.lungcan.2024.107791] [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: 10/06/2023] [Revised: 03/25/2024] [Accepted: 04/10/2024] [Indexed: 04/17/2024]
Abstract
OBJECTIVES With the increasing popularity of CT screening, more cases of early-stage lung cancer are being diagnosed. However, 24.5% of stage I non-small-cell lung cancer (NSCLC) patients still experience treatment failure post-surgery. Biomarkers to predict lung cancer patients at high risk of recurrence are needed. MATERIALS AND METHODS We collected protein mass spectrometry data from the Taiwan Lung Cancer Moonshot Project and performed bioinformatics analysis on proteins with differential expressions between tumor and adjacent normal tissues in 74 stage I lung adenocarcinoma (LUAD) cases, aiming to explore the tumor microenvironment related prognostic biomarkers. Findings were further validated in 6 external cohorts. RESULTS The analysis of differentially expressed proteins revealed that the most enriched categories of diseases and biological functions were cellular movement, immune cell trafficking, and cancer. Utilizing proteomic profiling of the tumor microenvironment, we identified five prognostic biomarkers (ADAM10, MIF, TEK, THBS2, MAOA). We then developed a risk score model, which independently predicted recurrence-free survival and overall survival in stage I LUAD. Patients with high risk scores experienced worse recurrence-free survival (adjusted hazard ratio = 8.28, p < 0.001) and overall survival (adjusted hazard ratio = 6.88, p = 0.013). Findings had been also validated in the external cohorts. CONCLUSION The risk score model derived from proteomic profiling of tumor microenvironment can be used to predict recurrence risk and prognosis of stage I LUAD.
Collapse
Affiliation(s)
- Yueh-Feng Lu
- Ph.D. Program in Translational Medicine, National Taiwan University and Academia Sinica, Taiwan; Division of Radiation Oncology, Department of Radiology, Far Eastern Memorial Hospital, New Taipei City, Taiwan
| | - Ya-Hsuan Chang
- Institute of Molecular and Genomic Medicine, National Health Research Institute, Taiwan.
| | - Yi-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan.
| | - Min-Shu Hsieh
- Department of Pathology, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Mong-Wei Lin
- Department of Surgery, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Hsao-Hsun Hsu
- Department of Surgery, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan
| | - Chia-Li Han
- Master Program in Clinical Genomics and Proteomics, College of Pharmacy, Taipei Medical University, Taipei, Taiwan.
| | - Yu-Ju Chen
- Institute of Chemistry, Academia Sinica, Taipei, Taiwan.
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University, Taiwan.
| | - Jin-Shing Chen
- Ph.D. Program in Translational Medicine, National Taiwan University and Academia Sinica, Taiwan; Department of Surgery, National Taiwan University Hospital and National Taiwan University College of Medicine, Taipei, Taiwan.
| | - Hsuan-Yu Chen
- Ph.D. Program in Translational Medicine, National Taiwan University and Academia Sinica, Taiwan; Doctoral Program in Microbial Genomics, National Chung Hsing University and Academia Sinica, Taiwan; Center for Cancer Research, Kaohsiung Medical University, Taiwan; Institute of Statistical Science, Academia Sinica, Taipei, Taiwan.
| |
Collapse
|
26
|
Liu J, Chang X, Qian L, Chen S, Xue Z, Wu J, Luo D, Huang B, Fan J, Guo T, Nie X. Proteomics-Derived Biomarker Panel Facilitates Distinguishing Primary Lung Adenocarcinomas With Intestinal or Mucinous Differentiation From Lung Metastatic Colorectal Cancer. Mol Cell Proteomics 2024; 23:100766. [PMID: 38608841 PMCID: PMC11092395 DOI: 10.1016/j.mcpro.2024.100766] [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: 09/12/2023] [Revised: 03/07/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024] Open
Abstract
The diagnosis of primary lung adenocarcinomas with intestinal or mucinous differentiation (PAIM) remains challenging due to the overlapping histomorphological, immunohistochemical (IHC), and genetic characteristics with lung metastatic colorectal cancer (lmCRC). This study aimed to explore the protein biomarkers that could distinguish between PAIM and lmCRC. To uncover differences between the two diseases, we used tandem mass tagging-based shotgun proteomics to characterize proteomes of formalin-fixed, paraffin-embedded tumor samples of PAIM (n = 22) and lmCRC (n = 17).Then three machine learning algorithms, namely support vector machine (SVM), random forest, and the Least Absolute Shrinkage and Selection Operator, were utilized to select protein features with diagnostic significance. These candidate proteins were further validated in an independent cohort (PAIM, n = 11; lmCRC, n = 19) by IHC to confirm their diagnostic performance. In total, 105 proteins out of 7871 proteins were significantly dysregulated between PAIM and lmCRC samples and well-separated two groups by Uniform Manifold Approximation and Projection. The upregulated proteins in PAIM were involved in actin cytoskeleton organization, platelet degranulation, and regulation of leukocyte chemotaxis, while downregulated ones were involved in mitochondrial transmembrane transport, vasculature development, and stem cell proliferation. A set of ten candidate proteins (high-level expression in lmCRC: CDH17, ATP1B3, GLB1, OXNAD1, LYST, FABP1; high-level expression in PAIM: CK7 (an established marker), NARR, MLPH, S100A14) was ultimately selected to distinguish PAIM from lmCRC by machine learning algorithms. We further confirmed using IHC that the five protein biomarkers including CDH17, CK7, MLPH, FABP1 and NARR were effective biomarkers for distinguishing PAIM from lmCRC. Our study depicts PAIM-specific proteomic characteristics and demonstrates the potential utility of new protein biomarkers for the differential diagnosis of PAIM and lmCRC. These findings may contribute to improving the diagnostic accuracy and guide appropriate treatments for these patients.
Collapse
Affiliation(s)
- Jiaying Liu
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaona Chang
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liujia Qian
- Center for ProtTalks, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Shuo Chen
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhangzhi Xue
- Center for ProtTalks, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Junhua Wu
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Danju Luo
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Huang
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Fan
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tiannan Guo
- Center for ProtTalks, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China.
| | - Xiu Nie
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
| |
Collapse
|
27
|
Zhang H, Liu J, Liu W, Chen H, Yu Z, Yuan Y, Wang P, Qin J. MHD-Net: Memory-Aware Hetero-Modal Distillation Network for Thymic Epithelial Tumor Typing With Missing Pathology Modality. IEEE J Biomed Health Inform 2024; 28:3003-3014. [PMID: 38470599 DOI: 10.1109/jbhi.2024.3376462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
Fusing multi-modal radiology and pathology data with complementary information can improve the accuracy of tumor typing. However, collecting pathology data is difficult since it is high-cost and sometimes only obtainable after the surgery, which limits the application of multi-modal methods in diagnosis. To address this problem, we propose comprehensively learning multi-modal radiology-pathology data in training, and only using uni-modal radiology data in testing. Concretely, a Memory-aware Hetero-modal Distillation Network (MHD-Net) is proposed, which can distill well-learned multi-modal knowledge with the assistance of memory from the teacher to the student. In the teacher, to tackle the challenge in hetero-modal feature fusion, we propose a novel spatial-differentiated hetero-modal fusion module (SHFM) that models spatial-specific tumor information correlations across modalities. As only radiology data is accessible to the student, we store pathology features in the proposed contrast-boosted typing memory module (CTMM) that achieves type-wise memory updating and stage-wise contrastive memory boosting to ensure the effectiveness and generalization of memory items. In the student, to improve the cross-modal distillation, we propose a multi-stage memory-aware distillation (MMD) scheme that reads memory-aware pathology features from CTMM to remedy missing modal-specific information. Furthermore, we construct a Radiology-Pathology Thymic Epithelial Tumor (RPTET) dataset containing paired CT and WSI images with annotations. Experiments on the RPTET and CPTAC-LUAD datasets demonstrate that MHD-Net significantly improves tumor typing and outperforms existing multi-modal methods on missing modality situations.
Collapse
|
28
|
Zhao D, Guo Y, Wei H, Jia X, Zhi Y, He G, Nie W, Huang L, Wang P, Laster KV, Liu Z, Wang J, Lee MH, Dong Z, Liu K. Multi-omics characterization of esophageal squamous cell carcinoma identifies molecular subtypes and therapeutic targets. JCI Insight 2024; 9:e171916. [PMID: 38652547 PMCID: PMC11141925 DOI: 10.1172/jci.insight.171916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 04/12/2024] [Indexed: 04/25/2024] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is the predominant form of esophageal cancer and is characterized by an unfavorable prognosis. To elucidate the distinct molecular alterations in ESCC and investigate therapeutic targets, we performed a comprehensive analysis of transcriptomics, proteomics, and phosphoproteomics data derived from 60 paired treatment-naive ESCC and adjacent nontumor tissue samples. Additionally, we conducted a correlation analysis to describe the regulatory relationship between transcriptomic and proteomic processes, revealing alterations in key metabolic pathways. Unsupervised clustering analysis of the proteomics data stratified patients with ESCC into 3 subtypes with different molecular characteristics and clinical outcomes. Notably, subtype III exhibited the worst prognosis and enrichment in proteins associated with malignant processes, including glycolysis and DNA repair pathways. Furthermore, translocase of inner mitochondrial membrane domain containing 1 (TIMMDC1) was validated as a potential prognostic molecule for ESCC. Moreover, integrated kinase-substrate network analysis using the phosphoproteome nominated candidate kinases as potential targets. In vitro and in vivo experiments further confirmed casein kinase II subunit α (CSNK2A1) as a potential kinase target for ESCC. These underlying data represent a valuable resource for researchers that may provide better insights into the biology and treatment of ESCC.
Collapse
Affiliation(s)
- Dengyun Zhao
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, China
| | - Yaping Guo
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
| | - Huifang Wei
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Xuechao Jia
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Yafei Zhi
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Guiliang He
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Wenna Nie
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Limeng Huang
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | - Penglei Wang
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
| | | | - Zhicai Liu
- Linzhou Cancer Hospital, Anyang, Henan, China
| | - Jinwu Wang
- Linzhou Cancer Hospital, Anyang, Henan, China
| | - Mee-Hyun Lee
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
- College of Korean Medicine, Dongshin University, Naju, Jeonnam, Republic of Korea
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, China
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, China
| | - Kangdong Liu
- Department of Pathophysiology, School of Basic Medical Sciences, Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan, China
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, Henan, China
- Tianjian Laboratory of Advanced Biomedical Sciences, Zhengzhou, Henan, China
- The Collaborative Innovation Center of Henan Province for Cancer Chemoprevention, Zhengzhou, Henan, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
- Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, Henan, China
| |
Collapse
|
29
|
Vallés-Martí A, de Goeij-de Haas RR, Henneman AA, Piersma SR, Pham TV, Knol JC, Verheij J, Dijk F, Halfwerk H, Giovannetti E, Jiménez CR, Bijlsma MF. Kinase activities in pancreatic ductal adenocarcinoma with prognostic and therapeutic avenues. Mol Oncol 2024. [PMID: 38650175 DOI: 10.1002/1878-0261.13625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 12/12/2023] [Accepted: 02/21/2024] [Indexed: 04/25/2024] Open
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a devastating disease with a limited number of known driver mutations but considerable cancer cell heterogeneity. Phosphoproteomics provides a direct read-out of aberrant signaling and the resultant clinically relevant phenotype. Mass spectrometry (MS)-based proteomics and phosphoproteomics were applied to 42 PDAC tumors. Data encompassed over 19 936 phosphoserine or phosphothreonine (pS/T; in 5412 phosphoproteins) and 1208 phosphotyrosine (pY; in 501 phosphoproteins) sites and a total of 3756 proteins. Proteome data identified three distinct subtypes with tumor intrinsic and stromal features. Subsequently, three phospho-subtypes were apparent: two tumor intrinsic (Phos1/2) and one stromal (Phos3), resembling known PDAC molecular subtypes. Kinase activity was analyzed by the Integrative iNferred Kinase Activity (INKA) scoring. Phospho-subtypes displayed differential phosphorylation signals and kinase activity, such as FGR and GSK3 activation in Phos1, SRC kinase family and EPHA2 in Phos2, and EGFR, INSR, MET, ABL1, HIPK1, JAK, and PRKCD in Phos3. Kinase activity analysis of an external PDAC cohort supported our findings and underscored the importance of PI3K/AKT and ERK pathways, among others. Interestingly, unfavorable patient prognosis correlated with higher RTK, PAK2, STK10, and CDK7 activity and high proliferation, whereas long survival was associated with MYLK and PTK6 activity, which was previously unknown. Subtype-associated activity profiles can guide therapeutic combination approaches in tumor and stroma-enriched tissues, and emphasize the critical role of parallel signaling pathways. In addition, kinase activity profiling identifies potential disease markers with prognostic significance.
Collapse
Affiliation(s)
- Andrea Vallés-Martí
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
- Cancer Biology, Cancer Center Amsterdam, The Netherlands
- Pharmacology Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Richard R de Goeij-de Haas
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Alex A Henneman
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Jaco C Knol
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Joanne Verheij
- Department of Pathology, Amsterdam University Medical Center, The Netherlands
| | - Frederike Dijk
- Department of Pathology, Amsterdam University Medical Center, The Netherlands
| | - Hans Halfwerk
- Department of Pathology, Amsterdam University Medical Center, The Netherlands
| | - Elisa Giovannetti
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- Pharmacology Laboratory, Cancer Center Amsterdam, The Netherlands
- Cancer Pharmacology Lab, AIRC Start-Up Unit, Fondazione Pisana per la Scienza, San Giuliano Terme, Italy
| | - Connie R Jiménez
- Department of Medical Oncology, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands
- OncoProteomics Laboratory, Cancer Center Amsterdam, The Netherlands
| | - Maarten F Bijlsma
- Cancer Biology, Cancer Center Amsterdam, The Netherlands
- Laboratory for Experimental Oncology and Radiobiology, Center for Experimental and Molecular Medicine, Amsterdam University Medical Center, University of Amsterdam, The Netherlands
| |
Collapse
|
30
|
Guan S, Chen X, Wei Y, Wang F, Xie W, Chen Y, Liang H, Zhu X, Yang Y, Fang W, Huang Y, Zhao H, Zhang X, Liu S, Zhuang W, Huang M, Wang X, Zhang L. Germline USP36 Mutation Confers Resistance to EGFR-TKIs by Upregulating MLLT3 Expression in Patients with Non-Small Cell Lung Cancer. Clin Cancer Res 2024; 30:1382-1396. [PMID: 38261467 DOI: 10.1158/1078-0432.ccr-23-2357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/07/2023] [Accepted: 01/19/2024] [Indexed: 01/25/2024]
Abstract
PURPOSE Although somatic mutations were explored in depth, limited biomarkers were found to predict the resistance of EGFR tyrosine kinase inhibitors (EGFR-TKI). Previous studies reported N6-methyladenosine (m6A) levels regulated response of EGFR-TKIs; whether the germline variants located in m6A sites affected resistance of EGFR-TKIs is still unknown. EXPERIMENTAL DESIGN Patients with non-small cell lung cancer (NSCLC) with EGFR-activating mutation were enrolled to investigate predictors for response of EGFR-TKIs using a genome-wide-variant-m6A analysis. Bioinformatics analysis and series of molecular biology assays were used to uncover the underlying mechanism. RESULTS We identified the germline mutation USP36 rs3744797 (C > A, K814N) was associated with survival of patients with NSCLC treated with gefitinib [median progression-free survival (PFS): CC vs. CA, 16.30 vs. 10.50 months, P < 0.0001, HR = 2.45] and erlotinib (median PFS: CC vs. CA, 14.13 vs. 9.47 months, P = 0.041, HR = 2.63). Functionally, the C > A change significantly upregulated USP36 expression by reducing its m6A level. Meanwhile, rs3744797_A (USP36 MUT) was found to facilitate proliferation, migration, and resistance to EGFR-TKIs via upregulating MLLT3 expression in vitro and in vivo. More importantly, MLLT3 and USP36 levels are tightly correlated in patients with NSCLC, which were associated with prognosis of patients. Mechanistically, USP36 MUT stabilized MLLT3 by deubiquitinating MLLT3 in nucleoli and consequently activating its downstream signaling (HIF1α and Snai). Furthermore, inhibition of MLLT3 alleviated USP36 variant-induced EGFR-TKIs resistance in EGFR-mutant NSCLC. CONCLUSIONS These findings characterized rs3744797 as an oncogenic variant in mediating EGFR-TKI resistance and tumor aggressiveness through deubiquitinating MLLT3, highlighting the variant as a predictive biomarker for EGFR-TKI response in NSCLC.
Collapse
Affiliation(s)
- Shaoxing Guan
- Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou City, Guangzhou, P.R. China
- Institute of Clinical Pharmacology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong Province, P.R. China
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou, Guangdong Province, P.R. China
| | - Xi Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Yuru Wei
- Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou City, Guangzhou, P.R. China
- Institute of Clinical Pharmacology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong Province, P.R. China
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou, Guangdong Province, P.R. China
| | - Fei Wang
- Ersha Department of Pharmacy, the Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, P.R. China
| | - Wen Xie
- Department of Pharmaceutical Sciences and Center for Pharmacogenetics, University of Pittsburgh School of Pharmacy, Pittsburgh, Pennsylvania
| | - Youhao Chen
- Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou City, Guangzhou, P.R. China
- Institute of Clinical Pharmacology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong Province, P.R. China
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou, Guangdong Province, P.R. China
| | - Heng Liang
- Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou City, Guangzhou, P.R. China
| | - Xia Zhu
- Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou City, Guangzhou, P.R. China
| | - Yunpeng Yang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Wenfeng Fang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Yan Huang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Hongyun Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Xiaoxu Zhang
- Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou City, Guangzhou, P.R. China
- Institute of Clinical Pharmacology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong Province, P.R. China
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou, Guangdong Province, P.R. China
| | - Shu Liu
- Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou City, Guangzhou, P.R. China
- Institute of Clinical Pharmacology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong Province, P.R. China
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou, Guangdong Province, P.R. China
| | - Wei Zhuang
- Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou City, Guangzhou, P.R. China
- Institute of Clinical Pharmacology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong Province, P.R. China
| | - Min Huang
- Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou City, Guangzhou, P.R. China
- Institute of Clinical Pharmacology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong Province, P.R. China
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou, Guangdong Province, P.R. China
| | - Xueding Wang
- Laboratory of Drug Metabolism and Pharmacokinetics, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou City, Guangzhou, P.R. China
- Institute of Clinical Pharmacology, School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, Guangdong Province, P.R. China
- Guangdong Provincial Key Laboratory of New Drug Design and Evaluation, Guangzhou, Guangdong Province, P.R. China
| | - Li Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| |
Collapse
|
31
|
Jiang W, Jaehnig EJ, Liao Y, Yaron-Barir TM, Johnson JL, Cantley LC, Zhang B. Illuminating the Dark Cancer Phosphoproteome Through a Machine-Learned Co-Regulation Map of 26,280 Phosphosites. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.19.585786. [PMID: 38562798 PMCID: PMC10983930 DOI: 10.1101/2024.03.19.585786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Mass spectrometry-based phosphoproteomics offers a comprehensive view of protein phosphorylation, but limited knowledge about the regulation and function of most phosphosites restricts our ability to extract meaningful biological insights from phosphoproteomics data. To address this, we combine machine learning and phosphoproteomic data from 1,195 tumor specimens spanning 11 cancer types to construct CoPheeMap, a network mapping the co-regulation of 26,280 phosphosites. Integrating network features from CoPheeMap into a machine learning model, CoPheeKSA, we achieve superior performance in predicting kinase-substrate associations. CoPheeKSA reveals 24,015 associations between 9,399 phosphosites and 104 serine/threonine kinases, including many unannotated phosphosites and under-studied kinases. We validate the accuracy of these predictions using experimentally determined kinase-substrate specificities. By applying CoPheeMap and CoPheeKSA to phosphosites with high computationally predicted functional significance and cancer-associated phosphosites, we demonstrate the effectiveness of these tools in systematically illuminating phosphosites of interest, revealing dysregulated signaling processes in human cancer, and identifying under-studied kinases as putative therapeutic targets.
Collapse
|
32
|
Holguin-Cruz JA, Bui JM, Jha A, Na D, Gsponer J. Widespread alteration of protein autoinhibition in human cancers. Cell Syst 2024; 15:246-263.e7. [PMID: 38366601 DOI: 10.1016/j.cels.2024.01.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 06/20/2023] [Accepted: 01/26/2024] [Indexed: 02/18/2024]
Abstract
Autoinhibition is a prevalent allosteric regulatory mechanism in signaling proteins. Reduced autoinhibition underlies the tumorigenic effect of some known cancer drivers, but whether autoinhibition is altered generally in cancer remains elusive. Here, we demonstrate that cancer-associated missense mutations, in-frame insertions/deletions, and fusion breakpoints are enriched within inhibitory allosteric switches (IASs) across all cancer types. Selection for IASs that are recurrently mutated in cancers identifies established and unknown cancer drivers. Recurrent missense mutations in IASs of these drivers are associated with distinct, cancer-specific changes in molecular signaling. For the specific case of PPP3CA, the catalytic subunit of calcineurin, we provide insights into the molecular mechanisms of altered autoinhibition by cancer mutations using biomolecular simulations, and demonstrate that such mutations are associated with transcriptome changes consistent with increased calcineurin signaling. Our integrative study shows that autoinhibition-modulating genetic alterations are positively selected for by cancer cells.
Collapse
Affiliation(s)
- Jorge A Holguin-Cruz
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jennifer M Bui
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Ashwani Jha
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Dokyun Na
- School of Integrative Engineering, Chung-Ang University, 84 Heukseok-ro, Dongjak-gu, Seoul 156-756, Republic of Korea
| | - Jörg Gsponer
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada.
| |
Collapse
|
33
|
Bateman NW, Abulez T, Soltis AR, McPherson A, Choi S, Garsed DW, Pandey A, Tian C, Hood BL, Conrads KA, Teng PN, Oliver J, Gist G, Mitchell D, Litzi TJ, Tarney CM, Crothers BA, Mhawech-Fauceglia P, Dalgard CL, Wilkerson MD, Pierobon M, Petricoin EF, Yan C, Meerzaman D, Bodelon C, Wentzensen N, Lee JSH, Huntsman DG, Shah S, Shriver CD, Phippen NT, Darcy KM, Bowtell DDL, Conrads TP, Maxwell GL. Proteogenomic analysis of enriched HGSOC tumor epithelium identifies prognostic signatures and therapeutic vulnerabilities. NPJ Precis Oncol 2024; 8:68. [PMID: 38480868 PMCID: PMC10937683 DOI: 10.1038/s41698-024-00519-8] [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: 06/28/2023] [Accepted: 01/15/2024] [Indexed: 03/17/2024] Open
Abstract
We performed a deep proteogenomic analysis of bulk tumor and laser microdissection enriched tumor cell populations from high-grade serous ovarian cancer (HGSOC) tissue specimens spanning a broad spectrum of purity. We identified patients with longer progression-free survival had increased immune-related signatures and validated proteins correlating with tumor-infiltrating lymphocytes in 65 tumors from an independent cohort of HGSOC patients, as well as with overall survival in an additional 126 HGSOC patient cohort. We identified that homologous recombination deficient (HRD) tumors are enriched in pathways associated with metabolism and oxidative phosphorylation that we validated in independent patient cohorts. We further identified that polycomb complex protein BMI-1 is elevated in HR proficient (HRP) tumors, that elevated BMI-1 correlates with poor overall survival in HRP but not HRD HGSOC patients, and that HRP HGSOC cells are uniquely sensitive to BMI-1 inhibition.
Collapse
Affiliation(s)
- Nicholas W Bateman
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
| | - Tamara Abulez
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Anthony R Soltis
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Andrew McPherson
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Seongmin Choi
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Dale W Garsed
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Ahwan Pandey
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
| | - Chunqiao Tian
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Brian L Hood
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Kelly A Conrads
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Pang-Ning Teng
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Julie Oliver
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Glenn Gist
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Dave Mitchell
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Tracy J Litzi
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
| | - Christopher M Tarney
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Barbara A Crothers
- The Joint Pathology Center, Defense Health Agency, National Capital Region Medical Directorate, Silver Spring, MD, USA
| | - Paulette Mhawech-Fauceglia
- Department of Anatomic Pathology, Division of Gynecologic Pathology, University of Southern California, Los Angeles, CA, USA
| | - Clifton L Dalgard
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Matthew D Wilkerson
- The American Genome Center, Collaborative Health Initiative Research Program, Department of Anatomy, Physiology and Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Mariaelena Pierobon
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Emanuel F Petricoin
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, VA, USA
| | - Chunhua Yan
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Daoud Meerzaman
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD, USA
| | - Clara Bodelon
- Division of Cancer Epidemiology and Genetics National Cancer Institute, Rockville, MD, USA
| | - Nicolas Wentzensen
- Division of Cancer Epidemiology and Genetics National Cancer Institute, Rockville, MD, USA
| | - Jerry S H Lee
- Ellison Institute for Transformative Medicine, University of Southern California, Los Angeles, CA, USA
| | - David G Huntsman
- Department of Pathology and Laboratory Medicine, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Sohrab Shah
- Department of Computational Oncology, Memorial Sloan Kettering Cancer Center, Manhattan, NY, USA
| | - Craig D Shriver
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - Neil T Phippen
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Kathleen M Darcy
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The Henry M. Jackson Foundation for the Advancement of Military Medicine Inc, Bethesda, MD, USA
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA
| | - David D L Bowtell
- Peter MacCallum Cancer Centre, Parkville, Melbourne, Victoria, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, Victoria, Australia
| | - Thomas P Conrads
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA.
| | - G Larry Maxwell
- Gynecologic Cancer Center of Excellence, Gynecologic Surgery and Obstetrics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA.
- The John P. Murtha Cancer Center Research Program, Department of Surgery, Uniformed Services University and Walter Reed National Military Medical Center, Bethesda, MD, USA.
- Women's Health Integrated Research Center, Women's Service Line, Inova Health System, Falls Church, VA, USA.
| |
Collapse
|
34
|
Rydzewski NR, Shi Y, Li C, Chrostek MR, Bakhtiar H, Helzer KT, Bootsma ML, Berg TJ, Harari PM, Floberg JM, Blitzer GC, Kosoff D, Taylor AK, Sharifi MN, Yu M, Lang JM, Patel KR, Citrin DE, Sundling KE, Zhao SG. A platform-independent AI tumor lineage and site (ATLAS) classifier. Commun Biol 2024; 7:314. [PMID: 38480799 PMCID: PMC10937974 DOI: 10.1038/s42003-024-05981-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 02/27/2024] [Indexed: 03/17/2024] Open
Abstract
Histopathologic diagnosis and classification of cancer plays a critical role in guiding treatment. Advances in next-generation sequencing have ushered in new complementary molecular frameworks. However, existing approaches do not independently assess both site-of-origin (e.g. prostate) and lineage (e.g. adenocarcinoma) and have minimal validation in metastatic disease, where classification is more difficult. Utilizing gradient-boosted machine learning, we developed ATLAS, a pair of separate AI Tumor Lineage and Site-of-origin models from RNA expression data on 8249 tumor samples. We assessed performance independently in 10,376 total tumor samples, including 1490 metastatic samples, achieving an accuracy of 91.4% for cancer site-of-origin and 97.1% for cancer lineage. High confidence predictions (encompassing the majority of cases) were accurate 98-99% of the time in both localized and remarkably even in metastatic samples. We also identified emergent properties of our lineage scores for tumor types on which the model was never trained (zero-shot learning). Adenocarcinoma/sarcoma lineage scores differentiated epithelioid from biphasic/sarcomatoid mesothelioma. Also, predicted lineage de-differentiation identified neuroendocrine/small cell tumors and was associated with poor outcomes across tumor types. Our platform-independent single-sample approach can be easily translated to existing RNA-seq platforms. ATLAS can complement and guide traditional histopathologic assessment in challenging situations and tumors of unknown primary.
Collapse
Affiliation(s)
- Nicholas R Rydzewski
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Yue Shi
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Chenxuan Li
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | | | - Hamza Bakhtiar
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Kyle T Helzer
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Matthew L Bootsma
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Tracy J Berg
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
| | - Paul M Harari
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - John M Floberg
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - Grace C Blitzer
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
| | - David Kosoff
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Amy K Taylor
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Marina N Sharifi
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Menggang Yu
- Department of Biostatistics and Medical Informatics, University of Wisconsin, Madison, WI, USA
| | - Joshua M Lang
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA
- Department of Medicine, University of Wisconsin, Madison, WI, USA
| | - Krishnan R Patel
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Deborah E Citrin
- Radiation Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Kaitlin E Sundling
- Department of Pathology and Laboratory Medicine, University of Wisconsin, Madison, WI, USA
- Wisconsin State Laboratory of Hygiene, University of Wisconsin, Madison, WI, USA
| | - Shuang G Zhao
- Department of Human Oncology, University of Wisconsin, Madison, WI, USA.
- Carbone Cancer Center, University of Wisconsin, Madison, WI, USA.
- William S. Middleton Veterans Hospital, Madison, WI, USA.
| |
Collapse
|
35
|
Kim KH, Migliozzi S, Koo H, Hong JH, Park SM, Kim S, Kwon HJ, Ha S, Garofano L, Oh YT, D'Angelo F, Kim CI, Kim S, Lee JY, Kim J, Hong J, Jang EH, Mathon B, Di Stefano AL, Bielle F, Laurenge A, Nesvizhskii AI, Hur EM, Yin J, Shi B, Kim Y, Moon KS, Kwon JT, Lee SH, Lee SH, Gwak HS, Lasorella A, Yoo H, Sanson M, Sa JK, Park CK, Nam DH, Iavarone A, Park JB. Integrated proteogenomic characterization of glioblastoma evolution. Cancer Cell 2024; 42:358-377.e8. [PMID: 38215747 PMCID: PMC10939876 DOI: 10.1016/j.ccell.2023.12.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 07/11/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024]
Abstract
The evolutionary trajectory of glioblastoma (GBM) is a multifaceted biological process that extends beyond genetic alterations alone. Here, we perform an integrative proteogenomic analysis of 123 longitudinal glioblastoma pairs and identify a highly proliferative cellular state at diagnosis and replacement by activation of neuronal transition and synaptogenic pathways in recurrent tumors. Proteomic and phosphoproteomic analyses reveal that the molecular transition to neuronal state at recurrence is marked by post-translational activation of the wingless-related integration site (WNT)/ planar cell polarity (PCP) signaling pathway and BRAF protein kinase. Consistently, multi-omic analysis of patient-derived xenograft (PDX) models mirror similar patterns of evolutionary trajectory. Inhibition of B-raf proto-oncogene (BRAF) kinase impairs both neuronal transition and migration capability of recurrent tumor cells, phenotypic hallmarks of post-therapy progression. Combinatorial treatment of temozolomide (TMZ) with BRAF inhibitor, vemurafenib, significantly extends the survival of PDX models. This study provides comprehensive insights into the biological mechanisms of glioblastoma evolution and treatment resistance, highlighting promising therapeutic strategies for clinical intervention.
Collapse
Affiliation(s)
- Kyung-Hee Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea; Proteomics Core Facility, Research Core Center, Research Institute, National Cancer Center, Goyang, Korea
| | - Simona Migliozzi
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Harim Koo
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea; Department of Biomedical Informatics, Korea University College of Medicine, Seoul, Korea; Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Jun-Hee Hong
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Seung Min Park
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Sooheon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Hyung Joon Kwon
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Seokjun Ha
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Luciano Garofano
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Young Taek Oh
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Fulvio D'Angelo
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Chan Il Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Seongsoo Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Ji Yoon Lee
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, Korea; Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Jiwon Kim
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, Korea; Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Jisoo Hong
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, Korea; Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea
| | - Eun-Hae Jang
- Laboratory of Neuroscience, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea
| | - Bertrand Mathon
- Service de Neurochirurgie, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France
| | - Anna-Luisa Di Stefano
- Institut de Neurologie, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), Equipe labellisée LNCC, Paris, France; Onconeurotek, AP-HP, Hôpital Pitié-Salpêtrière, F-75013 Paris, France; Department of Neurology, Foch Hospital, Suresnes, France
| | - Franck Bielle
- Institut de Neurologie, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), Equipe labellisée LNCC, Paris, France; Onconeurotek, AP-HP, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | - Alice Laurenge
- Institut de Neurologie, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), Equipe labellisée LNCC, Paris, France; Onconeurotek, AP-HP, Hôpital Pitié-Salpêtrière, F-75013 Paris, France
| | | | - Eun-Mi Hur
- Laboratory of Neuroscience, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul, Korea; BK21 Four Future Veterinary Medicine Leading Education & Research Center, College of Veterinary Medicine, Seoul National University, Seoul, Korea
| | - Jinlong Yin
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea; Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Bingyang Shi
- Henan-Macquarie University Joint Centre for Biomedical Innovation, School of Life Sciences, Henan University, Kaifeng, Henan, China
| | - Youngwook Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Kyung-Sub Moon
- Department of Neurosurgery, Chonnam National University Hwasun Hospital and Medical School, Hwasun, Korea
| | - Jeong Taik Kwon
- Department of Neurosurgery, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
| | - Shin Heon Lee
- Department of Neurosurgery, Chung-Ang University Hospital, Chung-Ang University College of Medicine, Seoul, Korea
| | - Seung Hoon Lee
- Department of Neurosurgery, Eulji University School of Medicine, Daejeon, Korea
| | - Ho Shin Gwak
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Anna Lasorella
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Biochemistry, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Heon Yoo
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea
| | - Marc Sanson
- Institut de Neurologie, AP-HP, Hôpitaux Universitaires La Pitié Salpêtrière - Charles Foix, Paris, France; Sorbonne Université, Inserm, CNRS, UMR S 1127, Paris Brain Institute (ICM), Equipe labellisée LNCC, Paris, France; Onconeurotek, AP-HP, Hôpital Pitié-Salpêtrière, F-75013 Paris, France.
| | - Jason K Sa
- Department of Biomedical Informatics, Korea University College of Medicine, Seoul, Korea; Department of Biomedical Sciences, Korea University College of Medicine, Seoul, Korea.
| | - Chul-Kee Park
- Deparment of Neurosurgery, Seoul National University College of Medicine, Seoul, Korea.
| | - Do-Hyun Nam
- Department of Neurosurgery and Samsung Advanced Institute for Health Sciences and Technology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
| | - Antonio Iavarone
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA; Department of Neurological Surgery and Department of Biochemistry, University of Miami Miller School of Medicine, Miami, FL, USA.
| | - Jong Bae Park
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang, Korea; Department of Clinical Research, Research Institute and Hospital, National Cancer Center, Goyang, Korea.
| |
Collapse
|
36
|
Yang X, Hu X, Yin J, Li W, Fu Y, Yang B, Fan J, Lu F, Qin T, Kang X, Zhuang X, Li F, Xiao R, Shi T, Song K, Li J, Chen G, Sun C. Comprehensive multi-omics analysis reveals WEE1 as a synergistic lethal target with hyperthermia through CDK1 super-activation. Nat Commun 2024; 15:2089. [PMID: 38453961 PMCID: PMC10920785 DOI: 10.1038/s41467-024-46358-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 02/23/2024] [Indexed: 03/09/2024] Open
Abstract
Hyperthermic intraperitoneal chemotherapy's role in ovarian cancer remains controversial, hindered by limited understanding of hyperthermia-induced tumor cellular changes. This limits developing potent combinatory strategies anchored in hyperthermic intraperitoneal therapy (HIPET). Here, we perform a comprehensive multi-omics study on ovarian cancer cells under hyperthermia, unveiling a distinct molecular panorama, primarily characterized by rapid protein phosphorylation changes. Based on the phospho-signature, we pinpoint CDK1 kinase is hyperactivated during hyperthermia, influencing the global signaling landscape. We observe dynamic, reversible CDK1 activity, causing replication arrest and early mitotic entry post-hyperthermia. Subsequent drug screening shows WEE1 inhibition synergistically destroys cancer cells with hyperthermia. An in-house developed miniaturized device confirms hyperthermia and WEE1 inhibitor combination significantly reduces tumors in vivo. These findings offer additional insights into HIPET, detailing molecular mechanisms of hyperthermia and identifying precise drug combinations for targeted treatment. This research propels the concept of precise hyperthermic intraperitoneal therapy, highlighting its potential against ovarian cancer.
Collapse
Affiliation(s)
- Xiaohang Yang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, PR China
| | - Xingyuan Hu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Jingjing Yin
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Wenting Li
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Shihezi University Shihezi, Xinjiang, 832000, PR China
| | - Yu Fu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Bin Yang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Junpeng Fan
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Funian Lu
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Tianyu Qin
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Xiaoyan Kang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Xucui Zhuang
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China
| | - Fuxia Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Shihezi University Shihezi, Xinjiang, 832000, PR China
| | - Rourou Xiao
- Department of Gynecology and Obstetrics, Zhongnan Hospital of Wuhan University, Wuhan, 430071, Hubei, PR China
| | - Tingyan Shi
- Ovarian Cancer Program, Department of Gynecologic Oncology, Zhongshan Hospital, Fudan University, Shanghai, 200032, PR China
| | - Kun Song
- Department of Obstetrics and Gynecology, Qilu Hospital of Shandong University, Jinan, 250012, PR China
| | - Jing Li
- Department of Gynecologic Oncology, Sun Yat-sen Memorial Hospital, 33 Yingfeng Road, Guangzhou, 510000, PR China.
| | - Gang Chen
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China.
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China.
| | - Chaoyang Sun
- Cancer Biology Research Center (Key Laboratory of the Ministry of Education), Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China.
- Department of Gynecology and Obstetrics, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430000, Hubei, PR China.
| |
Collapse
|
37
|
Chang E, An JY. Whole-genome doubling is a double-edged sword: the heterogeneous role of whole-genome doubling in various cancer types. BMB Rep 2024; 57:125-134. [PMID: 38449300 PMCID: PMC10979346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 02/01/2024] [Accepted: 02/01/2024] [Indexed: 03/08/2024] Open
Abstract
Whole-genome doubling (WGD), characterized by the duplication of an entire set of chromosomes, is commonly observed in various tumors, occurring in approximately 30-40% of patients with different cancer types. The effect of WGD on tumorigenesis varies depending on the context, either promoting or suppressing tumor progression. Recent advances in genomic technologies and large-scale clinical investigations have led to the identification of the complex patterns of genomic alterations underlying WGD and their functional consequences on tumorigenesis progression and prognosis. Our comprehensive review aims to summarize the causes and effects of WGD on tumorigenesis, highlighting its dualistic influence on cancer cells. We then introduce recent findings on WGD-associated molecular signatures and genetic aberrations and a novel subtype related to WGD. Finally, we discuss the clinical implications of WGD in cancer subtype classification and future therapeutic interventions. Overall, a comprehensive understanding of WGD in cancer biology is crucial to unraveling its complex role in tumorigenesis and identifying novel therapeutic strategies. [BMB Reports 2024; 57(3): 125-134].
Collapse
Affiliation(s)
- Eunhyong Chang
- Department of Integrated Biomedical and Life Science, Korea University, Seoul 02841, Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul 02841, Korea
| | - Joon-Yong An
- Department of Integrated Biomedical and Life Science, Korea University, Seoul 02841, Korea
- L-HOPE Program for Community-Based Total Learning Health Systems, Korea University, Seoul 02841, Korea
- School of Biosystem and Biomedical Science, College of Health Science, Korea University, Seoul 02841, Korea
| |
Collapse
|
38
|
Chen RJ, Ding T, Lu MY, Williamson DFK, Jaume G, Song AH, Chen B, Zhang A, Shao D, Shaban M, Williams M, Oldenburg L, Weishaupt LL, Wang JJ, Vaidya A, Le LP, Gerber G, Sahai S, Williams W, Mahmood F. Towards a general-purpose foundation model for computational pathology. Nat Med 2024; 30:850-862. [PMID: 38504018 DOI: 10.1038/s41591-024-02857-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 02/05/2024] [Indexed: 03/21/2024]
Abstract
Quantitative evaluation of tissue images is crucial for computational pathology (CPath) tasks, requiring the objective characterization of histopathological entities from whole-slide images (WSIs). The high resolution of WSIs and the variability of morphological features present significant challenges, complicating the large-scale annotation of data for high-performance applications. To address this challenge, current efforts have proposed the use of pretrained image encoders through transfer learning from natural image datasets or self-supervised learning on publicly available histopathology datasets, but have not been extensively developed and evaluated across diverse tissue types at scale. We introduce UNI, a general-purpose self-supervised model for pathology, pretrained using more than 100 million images from over 100,000 diagnostic H&E-stained WSIs (>77 TB of data) across 20 major tissue types. The model was evaluated on 34 representative CPath tasks of varying diagnostic difficulty. In addition to outperforming previous state-of-the-art models, we demonstrate new modeling capabilities in CPath such as resolution-agnostic tissue classification, slide classification using few-shot class prototypes, and disease subtyping generalization in classifying up to 108 cancer types in the OncoTree classification system. UNI advances unsupervised representation learning at scale in CPath in terms of both pretraining data and downstream evaluation, enabling data-efficient artificial intelligence models that can generalize and transfer to a wide range of diagnostically challenging tasks and clinical workflows in anatomic pathology.
Collapse
Affiliation(s)
- Richard J Chen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Tong Ding
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Ming Y Lu
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
| | - Drew F K Williamson
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Guillaume Jaume
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Andrew H Song
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Bowen Chen
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Andrew Zhang
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Health Sciences and Technology, Harvard-MIT, Cambridge, MA, USA
| | - Daniel Shao
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Health Sciences and Technology, Harvard-MIT, Cambridge, MA, USA
| | - Muhammad Shaban
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Mane Williams
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Lukas Oldenburg
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Luca L Weishaupt
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Health Sciences and Technology, Harvard-MIT, Cambridge, MA, USA
| | - Judy J Wang
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Anurag Vaidya
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Health Sciences and Technology, Harvard-MIT, Cambridge, MA, USA
| | - Long Phi Le
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Health Sciences and Technology, Harvard-MIT, Cambridge, MA, USA
| | - Georg Gerber
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Sharifa Sahai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Systems Biology, Harvard University, Cambridge, MA, USA
| | - Walt Williams
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Faisal Mahmood
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA.
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Cancer Data Science Program, Dana-Farber Cancer Institute, Boston, MA, USA.
- Harvard Data Science Initiative, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
39
|
Morel M, Long W. FBXL16 promotes cell growth and drug resistance in lung adenocarcinomas with KRAS mutation by stabilizing IRS1 and upregulating IRS1/AKT signaling. Mol Oncol 2024; 18:762-777. [PMID: 37983945 PMCID: PMC10920083 DOI: 10.1002/1878-0261.13554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/17/2023] [Accepted: 11/15/2023] [Indexed: 11/22/2023] Open
Abstract
Lung cancer is the leading cause of cancer-related deaths worldwide. Lung adenocarcinomas (LUADs) are a major subtype of non-small-cell lung cancers (NSCLCs). About 25% of LUADs harbor GTPase KRAS mutations associated with poor prognosis and limited treatment options. While encouraging tumor response to novel covalent inhibitors specifically targeting KRASG12C has been shown in the clinic, either intrinsic resistance exists or acquired therapeutic resistance arises upon treatment. There is an unmet need to identify new therapeutic targets for treating LUADs with activating KRAS mutations, particularly those with resistance to KRASG12C inhibitor(s). In this study, we have revealed that F-box/LRR-repeat protein 16 (FBXL16) is selectively upregulated in LUAD with KRAS mutations. It promotes LUAD cell growth and transforms lung epithelial cells. Importantly, FBXL16 depletion greatly enhances sensitivity to the KRASG12C inhibitor (sotorasib) in resistant cells by downregulating phosphatidylinositol 3-kinase (PI3K)/protein kinase B (PKB; also known as AKT) signaling. Mechanistically, FBXL16 upregulates insulin receptor substrate 1 (IRS1) protein stability, leading to an increase of IGF1/AKT signaling, thereby promoting cell growth and migration. Taken together, our study highlights the potential of FBXL16 as a therapeutic target for treating LUAD with KRAS activating mutations.
Collapse
Affiliation(s)
- Marion Morel
- Department of Biochemistry and Molecular Biology, Boonshoft School of MedicineWright State UniversityDaytonOHUSA
| | - Weiwen Long
- Department of Biochemistry and Molecular Biology, Boonshoft School of MedicineWright State UniversityDaytonOHUSA
| |
Collapse
|
40
|
Pastorino GA, Sheraj I, Huebner K, Ferrero G, Kunze P, Hartmann A, Hampel C, Husnugil HH, Maiuthed A, Gebhart F, Schlattmann F, Gulec Taskiran AE, Oral G, Palmisano R, Pardini B, Naccarati A, Erlenbach-Wuensch K, Banerjee S, Schneider-Stock R. A partial epithelial-mesenchymal transition signature for highly aggressive colorectal cancer cells that survive under nutrient restriction. J Pathol 2024; 262:347-361. [PMID: 38235615 DOI: 10.1002/path.6240] [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: 06/17/2023] [Revised: 10/12/2023] [Accepted: 11/21/2023] [Indexed: 01/19/2024]
Abstract
Partial epithelial-mesenchymal transition (p-EMT) has recently been identified as a hybrid state consisting of cells with both epithelial and mesenchymal characteristics and is associated with the migration, metastasis, and chemoresistance of cancer cells. Here, we describe the induction of p-EMT in starved colorectal cancer (CRC) cells and identify a p-EMT gene signature that can predict prognosis. Functional characterisation of starvation-induced p-EMT in HCT116, DLD1, and HT29 cells showed changes in proliferation, morphology, and drug sensitivity, supported by in vivo studies using the chorioallantoic membrane model. An EMT-specific quantitative polymerase chain reaction (qPCR) array was used to screen for deregulated genes, leading to the establishment of an in silico gene signature that was correlated with poor disease-free survival in CRC patients along with the CRC consensus molecular subtype CMS4. Among the significantly deregulated p-EMT genes, a triple-gene signature consisting of SERPINE1, SOX10, and epidermal growth factor receptor (EGFR) was identified. Starvation-induced p-EMT was characterised by increased migratory potential and chemoresistance, as well as E-cadherin processing and internalisation. Both gene signature and E-cadherin alterations could be reversed by the proteasomal inhibitor MG132. Spatially resolving EGFR expression with high-resolution immunofluorescence imaging identified a proliferation stop in starved CRC cells caused by EGFR internalisation. In conclusion, we have gained insight into a previously undiscovered EMT mechanism that may become relevant when tumour cells are under nutrient stress, as seen in early stages of metastasis. Targeting this process of tumour cell dissemination might help to prevent EMT and overcome drug resistance. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
Collapse
Affiliation(s)
- Gil A Pastorino
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Ilir Sheraj
- Department of Biological Sciences, Orta Dogu Teknik Universitesi, Ankara, Turkey
| | - Kerstin Huebner
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Giulio Ferrero
- Department of Clinical and Biological Sciences, University of Turin, Turin, Italy
| | - Philipp Kunze
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Arndt Hartmann
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Chuanpit Hampel
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | | | - Arnatchai Maiuthed
- Department of Pharmacology, Mahidol University, Bangkok, Thailand
- Centre of Biopharmaceutical Science for Healthy Ageing, Faculty of Pharmacy, Mahidol University, Bangkok, Thailand
| | - Florian Gebhart
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Fynn Schlattmann
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Aliye Ezgi Gulec Taskiran
- Department of Biological Sciences, Orta Dogu Teknik Universitesi, Ankara, Turkey
- Department of Molecular Biology and Genetics, Baskent University, Ankara, Turkey
| | - Goksu Oral
- Department of Biological Sciences, Orta Dogu Teknik Universitesi, Ankara, Turkey
| | - Ralph Palmisano
- Optical Imaging Competence Centre FAU OICE, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Barbara Pardini
- Italian Institute for Genomic Medicine (IIGM), c/o FPO-IRCCS Candiolo, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Alessio Naccarati
- Italian Institute for Genomic Medicine (IIGM), c/o FPO-IRCCS Candiolo, Turin, Italy
- Candiolo Cancer Institute, FPO-IRCCS, Turin, Italy
| | - Katharina Erlenbach-Wuensch
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| | - Sreeparna Banerjee
- Department of Biological Sciences, Orta Dogu Teknik Universitesi, Ankara, Turkey
- Cancer Systems Biology Laboratory (CanSyl), Orta Dogu Teknik Universitesi, Ankara, Turkey
| | - Regine Schneider-Stock
- Institute of Pathology, Universitätsklinikum Erlangen, Friedrich-Alexander Universität Erlangen-Nürnberg, Erlangen, Germany
| |
Collapse
|
41
|
Odintsov I, Sholl LM. Prognostic and predictive biomarkers in non-small cell lung carcinoma. Pathology 2024; 56:192-204. [PMID: 38199926 DOI: 10.1016/j.pathol.2023.11.006] [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: 10/17/2023] [Revised: 11/21/2023] [Accepted: 11/22/2023] [Indexed: 01/12/2024]
Abstract
Lung cancer is the most common cause of cancer-related deaths globally, with the highest mortality rates among both men and women. Most lung cancers are diagnosed at late stages, necessitating systemic therapy. Modern clinical management of lung cancer relies heavily upon application of biomarkers, which guide the selection of systemic treatment. Here, we provide an overview of currently approved and emerging biomarkers of non-small cell lung cancer (NSCLC), including EGFR, ALK, ROS1, RET, NTRK1-3, KRAS, BRAF, MET, ERBB2/HER2, NRG1, PD-L1, TROP2, and CEACAM5. For practical purposes, we divide these biomarkers into genomic and protein markers, based on the tested substrate. We review the biology and epidemiology of the genomic and proteomic biomarkers, discuss optimal diagnostic assays for their detection, and highlight their contribution to the contemporary clinical management of NSCLC.
Collapse
Affiliation(s)
- Igor Odintsov
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Lynette M Sholl
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
42
|
Jiang L, Qin J, Dai Y, Zhao S, Zhan Q, Cui P, Ren L, Wang X, Zhang R, Gao C, Zhou Y, Cai S, Wang G, Xie W, Tang X, Shi M, Ma F, Liu J, Wang T, Wang C, Svrcek M, Bardier-Dupas A, Emile JF, de Mestier L, Bachet JB, Nicolle R, Cros J, Laurent-Puig P, Wei M, Song B, Jing W, Guo S, Zheng K, Jiang H, Wang H, Deng X, Chen H, Tian Q, Wang S, Shi S, Jin G, Yin T, Fang H, Chen S, Shen B. Prospective observational study on biomarkers of response in pancreatic ductal adenocarcinoma. Nat Med 2024; 30:749-761. [PMID: 38287168 DOI: 10.1038/s41591-023-02790-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 12/21/2023] [Indexed: 01/31/2024]
Abstract
Adjuvant chemotherapy benefits patients with resected pancreatic ductal adenocarcinoma (PDAC), but the compromised physical state of post-operative patients can hinder compliance. Biomarkers that identify candidates for prompt adjuvant therapy are needed. In this prospective observational study, 1,171 patients with PDAC who underwent pancreatectomy were enrolled and extensively followed-up. Proteomic profiling of 191 patient samples unveiled clinically relevant functional protein modules. A proteomics-level prognostic risk model was established for PDAC, with its utility further validated using a publicly available external cohort. More importantly, through an interaction effect regression analysis leveraging both clinical and proteomic datasets, we discovered two biomarkers (NDUFB8 and CEMIP2), indicative of the overall sensitivity of patients with PDAC to adjuvant chemotherapy. The biomarkers were validated through immunohistochemistry on an internal cohort of 386 patients. Rigorous validation extended to two external multicentic cohorts-a French multicentric cohort (230 patients) and a cohort from two grade-A tertiary hospitals in China (466 patients)-enhancing the robustness and generalizability of our findings. Moreover, experimental validation through functional assays was conducted on PDAC cell lines and patient-derived organoids. In summary, our cohort-scale integration of clinical and proteomic data demonstrates the potential of proteomics-guided prognosis and biomarker-aided adjuvant chemotherapy for PDAC.
Collapse
Affiliation(s)
- Lingxi Jiang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jiejie Qin
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Yuting Dai
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shulin Zhao
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qian Zhan
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Peng Cui
- Burning Rock Biotech, Guangzhou, China
| | - Lingjie Ren
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Xuelong Wang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ruihong Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chenxu Gao
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yanting Zhou
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | | | | | - Xiaomei Tang
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Minmin Shi
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Fangfang Ma
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Jia Liu
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Ting Wang
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chaofu Wang
- Department of Pathology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Magali Svrcek
- Department of Pathology, Saint-Antoine Hospital - Sorbonne Universités, Paris, France
| | - Armelle Bardier-Dupas
- Department of Pathology, Pitié-Salpêtrière Hospital - Sorbonne Universités, Paris, France
| | - Jean Francois Emile
- Department of Pathology, Ambroise Paré Hospital - Université Saint Quentin en Yvelines, Paris, France
| | - Louis de Mestier
- Department of Pancreatology, Université Paris Cité - FHU MOSAIC, Beaujon Hospital, Clichy, France
| | - Jean-Baptiste Bachet
- Department of Gastroenterology, Pitié-Salpêtrière Hospital - Sorbonne Universités, Paris, France
| | - Remy Nicolle
- Université Paris Cité, FHU MOSAIC, Centre de Recherche sur l'Inflammation (CRI), INSERM, U1149, CNRS, ERL 8252, Paris, France
| | - Jerome Cros
- Department of Pathology, Université Paris Cité - FHU MOSAIC, Beaujon Hospital, Clichy, France
| | - Pierre Laurent-Puig
- Department of Biochemistry, Hôpital Européen Georges Pompidou, Centre de Recherche des Cordeliers, INSERM UMRS1138, CNRS, Sorbonne Université, USPC, Université Paris Cité, Equipe labellisée Ligue Nationale contre le cancer, CNRS, Paris, France
| | - Miaoyan Wei
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China
| | - Bin Song
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Wei Jing
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Shiwei Guo
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Kailian Zheng
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Hui Jiang
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
- Department of Pathology, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Huan Wang
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China
| | - Xiaxing Deng
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Hao Chen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Qiang Tian
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Shengyue Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, Shanghai, China.
| | - Gang Jin
- Department of Hepatobiliary Pancreatic Surgery, Changhai Hospital, Naval Medical University (Second Military Medical University), Shanghai, China.
| | - Tong Yin
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Hai Fang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Saijuan Chen
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Centre for Translational Medicine at Shanghai, Ruijin Hospital affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Research Institute of Pancreatic Diseases, Shanghai Key Laboratory of Translational Research for Pancreatic Neoplasms, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- State Key Laboratory of Systems Medicine for Cancer, Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai, China.
| |
Collapse
|
43
|
Petralia F, Ma W, Yaron TM, Caruso FP, Tignor N, Wang JM, Charytonowicz D, Johnson JL, Huntsman EM, Marino GB, Calinawan A, Evangelista JE, Selvan ME, Chowdhury S, Rykunov D, Krek A, Song X, Turhan B, Christianson KE, Lewis DA, Deng EZ, Clarke DJB, Whiteaker JR, Kennedy JJ, Zhao L, Segura RL, Batra H, Raso MG, Parra ER, Soundararajan R, Tang X, Li Y, Yi X, Satpathy S, Wang Y, Wiznerowicz M, González-Robles TJ, Iavarone A, Gosline SJC, Reva B, Robles AI, Nesvizhskii AI, Mani DR, Gillette MA, Klein RJ, Cieslik M, Zhang B, Paulovich AG, Sebra R, Gümüş ZH, Hostetter G, Fenyö D, Omenn GS, Cantley LC, Ma'ayan A, Lazar AJ, Ceccarelli M, Wang P. Pan-cancer proteogenomics characterization of tumor immunity. Cell 2024; 187:1255-1277.e27. [PMID: 38359819 PMCID: PMC10988632 DOI: 10.1016/j.cell.2024.01.027] [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: 04/26/2023] [Revised: 09/29/2023] [Accepted: 01/16/2024] [Indexed: 02/17/2024]
Abstract
Despite the successes of immunotherapy in cancer treatment over recent decades, less than <10%-20% cancer cases have demonstrated durable responses from immune checkpoint blockade. To enhance the efficacy of immunotherapies, combination therapies suppressing multiple immune evasion mechanisms are increasingly contemplated. To better understand immune cell surveillance and diverse immune evasion responses in tumor tissues, we comprehensively characterized the immune landscape of more than 1,000 tumors across ten different cancers using CPTAC pan-cancer proteogenomic data. We identified seven distinct immune subtypes based on integrative learning of cell type compositions and pathway activities. We then thoroughly categorized unique genomic, epigenetic, transcriptomic, and proteomic changes associated with each subtype. Further leveraging the deep phosphoproteomic data, we studied kinase activities in different immune subtypes, which revealed potential subtype-specific therapeutic targets. Insights from this work will facilitate the development of future immunotherapy strategies and enhance precision targeting with existing agents.
Collapse
Affiliation(s)
- Francesca Petralia
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| | - Weiping Ma
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA; Columbia University Vagelos College of Physicians and Surgeons, New York, NY 10032, USA
| | - Francesca Pia Caruso
- BIOGEM Institute of Molecular Biology and Genetics, 83031 Ariano Irpino, Italy; Department of Electrical Engineering and Information Technologies, University of Naples "Federico II", Naples, Italy
| | - Nicole Tignor
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Joshua M Wang
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Daniel Charytonowicz
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Emily M Huntsman
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Giacomo B Marino
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Anna Calinawan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John Erol Evangelista
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Myvizhi Esai Selvan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Shrabanti Chowdhury
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Dmitry Rykunov
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Xiaoyu Song
- Institute for Healthcare Delivery Science, Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Berk Turhan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Karen E Christianson
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - David A Lewis
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Eden Z Deng
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Daniel J B Clarke
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Lei Zhao
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Rossana Lazcano Segura
- Departments of Pathology & Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Harsh Batra
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Maria Gabriela Raso
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Edwin Roger Parra
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rama Soundararajan
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Ximing Tang
- Department of Translational Molecular Pathology, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Yize Li
- Department of Medicine, Washington University in St. Louis, St. Louis, MO 63110, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63108, USA
| | - Xinpei Yi
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shankha Satpathy
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Ying Wang
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Maciej Wiznerowicz
- Department of Medical Biotechnology, Poznan University of Medical Sciences, 61-701 Poznań, Poland; International Institute for Molecular Oncology, 60-203 Poznań, Poland; Department of Oncology, Heliodor Swiecicki Clinical Hospital, 60-203 Poznań, Poland
| | - Tania J González-Robles
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Antonio Iavarone
- Department of Neurological Surgery, Department of Biochemistry, Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, USA
| | - Sara J C Gosline
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Boris Reva
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ana I Robles
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA
| | - Alexey I Nesvizhskii
- Departments of Pathology and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - D R Mani
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Michael A Gillette
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Robert J Klein
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Marcin Cieslik
- Departments of Pathology and Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
| | - Bing Zhang
- Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Robert Sebra
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zeynep H Gümüş
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Lipschultz Precision Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Galen Hostetter
- Pathology and Biorepository Core, Van Andel Research Institute, Grand Rapids, MI 49503, USA
| | - David Fenyö
- Institute for Systems Genetics, New York University Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Gilbert S Omenn
- Departments of Computational Medicine & Bioinformatics, Internal Medicine, Human Genetics, & Environmental Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Avi Ma'ayan
- Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Alexander J Lazar
- Departments of Pathology & Genomic Medicine, the University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Michele Ceccarelli
- Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA; Department of Public Health Sciences, University of Miami, Miami, FL, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
| |
Collapse
|
44
|
Feng S, Calinawan A, Pugliese P, Wang P, Ceccarelli M, Petralia F, Gosline SJC. Decomprolute is a benchmarking platform designed for multiomics-based tumor deconvolution. CELL REPORTS METHODS 2024; 4:100708. [PMID: 38412834 PMCID: PMC10921018 DOI: 10.1016/j.crmeth.2024.100708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 10/23/2023] [Accepted: 01/18/2024] [Indexed: 02/29/2024]
Abstract
Tumor deconvolution enables the identification of diverse cell types that comprise solid tumors. To date, however, both the algorithms developed to deconvolve tumor samples, and the gold-standard datasets used to assess the algorithms are geared toward the analysis of gene expression (e.g., RNA sequencing) rather than protein levels. Despite the popularity of gene expression datasets, protein levels often provide a more accurate view of rare cell types. To facilitate the use, development, and reproducibility of multiomic deconvolution algorithms, we introduce Decomprolute, a Common Workflow Language framework that leverages containerization to compare tumor deconvolution algorithms across multiomic datasets. Decomprolute incorporates the large-scale multiomic datasets produced by the Clinical Proteomic Tumor Analysis Consortium (CPTAC), which include matched mRNA expression and proteomic data from thousands of tumors across multiple cancer types to build a fully open-source, containerized proteogenomic tumor deconvolution benchmarking platform. http://pnnl-compbio.github.io/decomprolute.
Collapse
Affiliation(s)
- Song Feng
- Pacific Northwest National Laboratory, Seattle, WA, USA
| | - Anna Calinawan
- Icahn School of Medicine at Mount Sinai School, New York, NY, USA
| | | | - Pei Wang
- Icahn School of Medicine at Mount Sinai School, New York, NY, USA
| | | | | | | |
Collapse
|
45
|
Murchan P, Baird AM, Ó Broin P, Sheils O, Finn SP. Surrogate Biomarker Prediction from Whole-Slide Images for Evaluating Overall Survival in Lung Adenocarcinoma. Diagnostics (Basel) 2024; 14:462. [PMID: 38472935 DOI: 10.3390/diagnostics14050462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Recent advances in computational pathology have shown potential in predicting biomarkers from haematoxylin and eosin (H&E) whole-slide images (WSI). However, predicting the outcome directly from WSIs remains a substantial challenge. In this study, we aimed to investigate how gene expression, predicted from WSIs, could be used to evaluate overall survival (OS) in patients with lung adenocarcinoma (LUAD). METHODS Differentially expressed genes (DEGs) were identified from The Cancer Genome Atlas (TCGA)-LUAD cohort. Cox regression analysis was performed on DEGs to identify the gene prognostics of OS. Attention-based multiple instance learning (AMIL) models were trained to predict the expression of identified prognostic genes from WSIs using the TCGA-LUAD dataset. Models were externally validated in the Clinical Proteomic Tumour Analysis Consortium (CPTAC)-LUAD dataset. The prognostic value of predicted gene expression values was then compared to the true gene expression measurements. RESULTS The expression of 239 prognostic genes could be predicted in TCGA-LUAD with cross-validated Pearson's R > 0.4. Predicted gene expression demonstrated prognostic performance, attaining a cross-validated concordance index of up to 0.615 in TCGA-LUAD through Cox regression. In total, 36 genes had predicted expression in the external validation cohort that was prognostic of OS. CONCLUSIONS Gene expression predicted from WSIs is an effective method of evaluating OS in patients with LUAD. These results may open up new avenues of cost- and time-efficient prognosis assessment in LUAD treatment.
Collapse
Affiliation(s)
- Pierre Murchan
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- The SFI Centre for Research Training in Genomics Data Science, University of Galway, H91 CF50 Galway, Ireland
- Trinity St. James's Cancer Institute (TSJCI), St. James's Hospital, D08 RX0X Dublin, Ireland
| | - Anne-Marie Baird
- Trinity St. James's Cancer Institute (TSJCI), St. James's Hospital, D08 RX0X Dublin, Ireland
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D02 A440 Dublin, Ireland
| | - Pilib Ó Broin
- School of Mathematical & Statistical Sciences, University of Galway, H91 TK33 Galway, Ireland
| | - Orla Sheils
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Trinity St. James's Cancer Institute (TSJCI), St. James's Hospital, D08 RX0X Dublin, Ireland
| | - Stephen P Finn
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Trinity St. James's Cancer Institute (TSJCI), St. James's Hospital, D08 RX0X Dublin, Ireland
- Department of Histopathology, St. James's Hospital, James's Street, D08 X4RX Dublin, Ireland
| |
Collapse
|
46
|
Long R, Abulimiti N, Wang X. Proteomics-based clustering of lung adenocarcinoma identifies three subtypes with significantly different clinical and molecular features. Clin Transl Oncol 2024; 26:538-548. [PMID: 37603150 DOI: 10.1007/s12094-023-03275-6] [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: 06/12/2023] [Accepted: 07/03/2023] [Indexed: 08/22/2023]
Abstract
BACKGROUND Lung adenocarcinoma (LUAD) is a predominant subtype of lung cancer. Although molecular classification of LUAD has been widely explored, proteomics-based subtyping of LUAD remains scarce. METHODS We proposed a subtyping method for LUAD based on the expression profiles of 500 proteins with the largest expression variability across LUAD. Furthermore, we comprehensively compared molecular and clinical features among the LUAD subtypes. RESULTS Consensus clustering identified three subtypes of LUAD, namely MtE, DrE, and StE. We demonstrated this subtyping method to be reproducible by analyzing two independent LUAD cohorts. MtE was characterized by high enrichment of metabolic pathways, high EGFR mutation rate, low stemness, proliferation, invasion, metastasis and inflammation signatures, favorable prognosis; DrE was characterized by high enrichment of DNA repair pathways, high TP53 mutation rate, and high levels of genomic instability, stemness, proliferation, and intratumor heterogeneity (ITH); and StE was characterized by high enrichment of stroma-related pathways, high KRAS mutation rate, and low levels of genomic instability. CONCLUSIONS The proteomics-based clustering analysis identified three LUAD subtypes with significantly different molecular and clinical properties. The novel subtyping method offers new perspectives on the cancer biology and holds promise in improving the clinical management of LUAD.
Collapse
Affiliation(s)
- Rongzhuo Long
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China
| | - Nayila Abulimiti
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China
| | - Xiaosheng Wang
- Biomedical Informatics Research Lab, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
- Cancer Genomics Research Center, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
- Big Data Research Institute, China Pharmaceutical University, Nanjing, 211198, China.
| |
Collapse
|
47
|
Hijazo‐Pechero S, Alay A, Cordero D, Marín R, Vilariño N, Palmero R, Brenes J, Montalban‐Casafont A, Nadal E, Solé X. Transcriptional analysis of landmark molecular pathways in lung adenocarcinoma results in a clinically relevant classification with potential therapeutic implications. Mol Oncol 2024; 18:453-470. [PMID: 37943164 PMCID: PMC10850798 DOI: 10.1002/1878-0261.13550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/11/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023] Open
Abstract
Lung adenocarcinoma (LUAD) is a molecularly heterogeneous disease. In addition to genomic alterations, cancer transcriptional profiling can be helpful to tailor cancer treatment and to estimate each patient's outcome. Transcriptional activity levels of 50 molecular pathways were inferred in 4573 LUAD patients using Gene Set Variation Analysis (GSVA) method. Seven LUAD subtypes were defined and independently validated based on the combined behavior of the studied pathways: AD (adenocarcinoma subtype) 1-7. AD1, AD4, and AD5 subtypes were associated with better overall survival. AD1 and AD4 subtypes were enriched in epidermal growth factor receptor (EGFR) mutations, whereas AD2 and AD6 showed higher tumor protein p53 (TP53) alteration frequencies. AD2 and AD6 subtypes correlated with higher genome instability, proliferation-related pathway expression, and specific sensitivity to chemotherapy, based on data from LUAD cell lines. LUAD subtypes were able to predict immunotherapy response in addition to CD274 (PD-L1) gene expression and tumor mutational burden (TMB). AD2 and AD4 subtypes were associated with potential resistance and response to immunotherapy, respectively. Thus, analysis of transcriptomic data could improve patient stratification beyond genomics and single biomarkers (i.e., PD-L1 and TMB) and may lay the foundation for more personalized treatment avenues, especially in driver-negative LUAD.
Collapse
Affiliation(s)
- Sara Hijazo‐Pechero
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO)L'Hospitalet de LlobregatBarcelonaSpain
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de LlobregatBarcelonaSpain
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
| | - Ania Alay
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO)L'Hospitalet de LlobregatBarcelonaSpain
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de LlobregatBarcelonaSpain
| | - David Cordero
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO)L'Hospitalet de LlobregatBarcelonaSpain
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de LlobregatBarcelonaSpain
| | - Raúl Marín
- Unit of Bioinformatics for Precision Oncology, Catalan Institute of Oncology (ICO)L'Hospitalet de LlobregatBarcelonaSpain
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de LlobregatBarcelonaSpain
| | - Noelia Vilariño
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de LlobregatBarcelonaSpain
- Thoracic Oncology Unit, Department of Medical Oncology, Catalan Institute of Oncology (ICO)L'Hospitalet de LlobregatBarcelonaSpain
- Neuro‐Oncology Unit, Catalan Institute of Oncology (ICO)L'Hospitalet de LlobregatBarcelonaSpain
| | - Ramón Palmero
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de LlobregatBarcelonaSpain
- Thoracic Oncology Unit, Department of Medical Oncology, Catalan Institute of Oncology (ICO)L'Hospitalet de LlobregatBarcelonaSpain
| | - Jesús Brenes
- Thoracic Oncology Unit, Department of Medical Oncology, Catalan Institute of Oncology (ICO)L'Hospitalet de LlobregatBarcelonaSpain
| | - Aina Montalban‐Casafont
- Molecular Biology CORE, Center for Biomedical Diagnostics (CDB)Hospital Clínic de BarcelonaSpain
| | - Ernest Nadal
- Preclinical and Experimental Research in Thoracic Tumors (PrETT), Molecular Mechanisms and Experimental Therapy in Oncology Program (Oncobell), Bellvitge Biomedical Research Institute (IDIBELL)L'Hospitalet de LlobregatBarcelonaSpain
- Thoracic Oncology Unit, Department of Medical Oncology, Catalan Institute of Oncology (ICO)L'Hospitalet de LlobregatBarcelonaSpain
| | - Xavier Solé
- Translational Genomics and Targeted Therapies in Solid TumorsAugust Pi i Sunyer Biomedical Research Institute (IDIBAPS)BarcelonaSpain
- Molecular Biology CORE, Center for Biomedical Diagnostics (CDB)Hospital Clínic de BarcelonaSpain
| |
Collapse
|
48
|
Liu Y, Li Z, Meng Q, Ning A, Zhou S, Li S, Tao X, Wu Y, Chen Q, Tian T, Zhang L, Cui J, Mao L, Chu M. Identification of the consistently differential expressed hub mRNAs and proteins in lung adenocarcinoma and construction of the prognostic signature: a multidimensional analysis. Int J Surg 2024; 110:1052-1067. [PMID: 38016140 PMCID: PMC10871637 DOI: 10.1097/js9.0000000000000943] [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: 08/29/2023] [Accepted: 11/12/2023] [Indexed: 11/30/2023]
Abstract
BACKGROUND This study aimed to elucidate the consistency of differentially expressed hub mRNAs and proteins in lung adenocarcinoma (LUAD) across populations and to construct a comprehensive LUAD prognostic signature. METHODS The transcriptomic and proteomics data from different populations were standardized and analyzed using the same criteria to identify the consistently differential expressed mRNAs and proteins across genders and races. We then integrated prognosis-related mRNAs with clinical, pathological, and EGFR (epidermal growth factor receptor) mutation data to construct a survival model, subsequently validating it across populations. Through plasma proteomics, plasma proteins that consistently differential expressed with LUAD tissues were screened and validated, with their associations discerned by measuring expressions in tumor tissues and tumor vascular normalization. RESULTS The consistency rate of differentially expressed mRNAs and proteins was ~20-40%, with ethnic factors leading to about 40-60% consistency of differentially expressed mRNA or protein across populations. The survival model based on the identified eight hub mRNAs as well as stage, smoking status, and EGFR mutations, demonstrated good prognostic prediction capabilities in both Western and East Asian populations, with a higher number of unfavorable variables indicating poorer LUAD prognosis. Notably, GPI expression in tumor tissues was inversely correlated with vascular normalization and positively correlated with plasma GPI expression. CONCLUSION Our study underscores the significance of integrating transcriptomics and proteomics data, emphasizing the need to account for genetic diversity among ethnic groups. The developed survival model may offer a holistic perspective on LUAD progression, enhancing prognosis and therapeutic strategies.
Collapse
Affiliation(s)
- Yiran Liu
- Department of Epidemiology, School of Public Health, Nantong University
| | - Zhenyu Li
- Department of Epidemiology, School of Public Health, Nantong University
| | - Qianyao Meng
- Department of Global Health and Population, School of Public Health, Harvard University, Boston, USA
| | - Anhui Ning
- Department of Epidemiology, School of Public Health, Nantong University
| | - Shenxuan Zhou
- Department of Epidemiology, School of Public Health, Nantong University
| | - Siqi Li
- Department of Epidemiology, School of Public Health, Nantong University
| | - Xiaobo Tao
- Department of Epidemiology, School of Public Health, Nantong University
| | - Yutong Wu
- Department of Epidemiology, School of Public Health, Nantong University
| | - Qiong Chen
- Department of Epidemiology, School of Public Health, Nantong University
| | - Tian Tian
- Department of Epidemiology, School of Public Health, Nantong University
| | - Lei Zhang
- Department of Epidemiology, School of Public Health, Nantong University
| | - Jiahua Cui
- Department of Epidemiology, School of Public Health, Nantong University
| | - Liping Mao
- Department of Oncology, Affiliated Nantong Hospital of Shanghai University (The Sixth People’s Hospital of Nantong), Nantong, Jiangsu, People’s Republic of China
| | - Minjie Chu
- Department of Epidemiology, School of Public Health, Nantong University
| |
Collapse
|
49
|
Lv L, Ren S, Jiang H, Yan R, Chen W, Yan R, Dong J, Shao L, Yu Y. The oral administration of Lacticaseibacillus casei Shirota alleviates acetaminophen-induced liver injury through accelerated acetaminophen metabolism via the liver-gut axis in mice. mSphere 2024; 9:e0067223. [PMID: 38193757 PMCID: PMC10826347 DOI: 10.1128/msphere.00672-23] [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: 10/31/2023] [Accepted: 12/03/2023] [Indexed: 01/10/2024] Open
Abstract
Acetaminophen is a widely used antipyretic and analgesic drug, and its overdose is the leading cause of drug-induced acute liver failure. This study aimed to investigate the effect and mechanism of Lacticaseibacillus casei Shirota (LcS), an extensively used and highly studied probiotic, on acetaminophen-induced acute liver injury. C57BL/6 mice were gavaged with LcS suspension or saline once daily for 7 days before acute liver injury was induced via intraperitoneal injection of 300 mg/kg acetaminophen. The results showed that LcS significantly decreased acetaminophen-induced liver and ileum injury, as demonstrated by reductions in the increases in aspartate aminotransferase, total bile acids, total bilirubin, indirect bilirubin, and hepatic cell necrosis. Moreover, LcS alleviated acetaminophen-induced intestinal mucosal permeability, decreased serum IL-1α and lipopolysaccharide levels, and elevated serum eosinophil chemokine (eotaxin) and hepatic glutathione levels. Furthermore, analysis of the gut microbiota and metabolome showed that LcS reduced the acetaminophen-enriched levels of Cyanobacteria, Oxyphotobacteria, long-chain fatty acids, cholesterol, and sugars in the gut. Additionally, the transcriptomic and proteomic results showed that LcS mitigated the decrease in metabolic and immune pathways as well as glutathione formation during acetaminophen-induced acute liver injury. This is the first study showing that pretreatment with LcS alleviates acetaminophen-enriched acute liver injury, and it provides a reference for the application of LcS.IMPORTANCEAcetaminophen is the most frequently used antipyretic analgesic worldwide. As a result, overdoses easily occur and lead to drug-induced acute liver injury, which quickly progresses to liver failure with a mortality of 60%-80% if not corrected in time. The current emergency treatment for overused acetaminophen needs to be administered within 8 hours to avoid liver injury or even liver failure. Therefore, developing preventive strategies for liver injury during planned acetaminophen medication is particularly important, preferably nonpharmacological methods. Lacticaseibacillus casei Shirota (LcS) is a famous probiotic that has been used for many years. Our study found that LcS significantly alleviated acetaminophen-induced acute liver injury, especially acetaminophen-induced liver injury toward fulminant hepatic failure. Here, we elucidated the function and potential mechanisms of LcS in alleviating acetaminophen-induced acute liver injury, hoping it will provide preventive strategies to people during acetaminophen treatment.
Collapse
Affiliation(s)
- Longxian Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Siqi Ren
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Huiyong Jiang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Ren Yan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
| | - Wenyi Chen
- School of Clinical Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Ruiyi Yan
- School of Clinical Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Jinming Dong
- School of Clinical Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Li Shao
- The Affiliated Hospital of Hangzhou Normal University, Institute of Translational Medicine, Hangzhou Normal University, Hangzhou, Zhejiang, China
| | - Ying Yu
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang Province, School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, China
| |
Collapse
|
50
|
Zhang K, Zakeri A, Alban T, Dong J, Ta HM, Zalavadia AH, Branicky A, Zhao H, Juric I, Husich H, Parthasarathy PB, Rupani A, Drazba JA, Chakraborty AA, Ching-Cheng Huang S, Chan T, Avril S, Wang LL. VISTA promotes the metabolism and differentiation of myeloid-derived suppressor cells by STAT3 and polyamine-dependent mechanisms. Cell Rep 2024; 43:113661. [PMID: 38175754 PMCID: PMC10851928 DOI: 10.1016/j.celrep.2023.113661] [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: 06/14/2023] [Revised: 10/20/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
Myeloid-derived suppressor cells (MDSCs) impair antitumor immune responses. Identifying regulatory circuits during MDSC development may bring new opportunities for therapeutic interventions. We report that the V-domain suppressor of T cell activation (VISTA) functions as a key enabler of MDSC differentiation. VISTA deficiency reduced STAT3 activation and STAT3-dependent production of polyamines, which causally impaired mitochondrial respiration and MDSC expansion. In both mixed bone marrow (BM) chimera mice and myeloid-specific VISTA conditional knockout mice, VISTA deficiency significantly reduced tumor-associated MDSCs but expanded monocyte-derived dendritic cells (DCs) and enhanced T cell-mediated tumor control. Correlated expression of VISTA and arginase-1 (ARG1), a key enzyme supporting polyamine biosynthesis, was observed in multiple human cancer types. In human endometrial cancer, co-expression of VISTA and ARG1 on tumor-associated myeloid cells is associated with poor survival. Taken together, these findings unveil the VISTA/polyamine axis as a central regulator of MDSC differentiation and warrant therapeutically targeting this axis for cancer immunotherapy.
Collapse
Affiliation(s)
- Keman Zhang
- Department of Translational Hematology and Oncology Research, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Amin Zakeri
- Department of Translational Hematology and Oncology Research, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Tyler Alban
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Juan Dong
- Department of Translational Hematology and Oncology Research, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Hieu M Ta
- Department of Translational Hematology and Oncology Research, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Ajay H Zalavadia
- Imaging Core Facility, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Andrelie Branicky
- Imaging Core Facility, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Haoxin Zhao
- Imaging Core Facility, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Ivan Juric
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Hanna Husich
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Prerana B Parthasarathy
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Amit Rupani
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Judy A Drazba
- Imaging Core Facility, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Abhishek A Chakraborty
- Department of Cancer Biology, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Stanley Ching-Cheng Huang
- Department of Pathology, University Hospitals Cleveland Medical Center, and Case Western Reserve University School of Medicine, Cleveland, OH, USA; Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Timothy Chan
- Center for Immunotherapy and Precision Immuno-Oncology, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA
| | - Stefanie Avril
- Department of Pathology, University Hospitals Cleveland Medical Center, and Case Western Reserve University School of Medicine, Cleveland, OH, USA; Case Comprehensive Cancer Center, Cleveland, OH, USA
| | - Li Lily Wang
- Department of Translational Hematology and Oncology Research, Cleveland Clinic Foundation, 9500 Euclid Avenue, Cleveland, OH, USA.
| |
Collapse
|