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Hu C, Song J, Kwok T, Nguyen EV, Shen X, Daly RJ. Proteome-based molecular subtyping and therapeutic target prediction in gastric cancer. Mol Oncol 2024; 18:1437-1459. [PMID: 38627210 PMCID: PMC11161736 DOI: 10.1002/1878-0261.13654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 03/12/2024] [Accepted: 04/05/2024] [Indexed: 06/09/2024] Open
Abstract
Different molecular classifications for gastric cancer (GC) have been proposed based on multi-omics platforms with the long-term goal of improved precision treatment. However, the GC (phospho)proteome remains incompletely characterized, particularly at the level of tyrosine phosphorylation. In addition, previous multiomics-based stratification of patient cohorts has lacked identification of corresponding cell line models and comprehensive validation of broad or subgroup-selective therapeutic targets. To address these knowledge gaps, we applied a reverse approach, undertaking the most comprehensive (phospho)proteomic analysis of GC cell lines to date and cross-validating this using publicly available data. Mass spectrometry (MS)-based (phospho)proteomic and tyrosine phosphorylation datasets were subjected to individual or integrated clustering to identify subgroups that were subsequently characterized in terms of enriched molecular processes and pathways. Significant congruence was detected between cell line proteomic and specific patient-derived transcriptomic subclassifications. Many protein kinases exhibiting 'outlier' expression or phosphorylation in the cell line dataset exhibited genomic aberrations in patient samples and association with poor prognosis, with casein kinase I isoform delta/epsilon (CSNK1D/E) being experimentally validated as potential therapeutic targets. Src family kinases were predicted to be commonly hyperactivated in GC cell lines, consistent with broad sensitivity to the next-generation Src inhibitor eCF506. In addition, phosphoproteomic and integrative clustering segregated the cell lines into two subtypes, with epithelial-mesenchyme transition (EMT) and proliferation-associated processes enriched in one, designated the EMT subtype, and metabolic pathways, cell-cell junctions, and the immune response dominating the features of the other, designated the metabolism subtype. Application of kinase activity prediction algorithms and interrogation of gene dependency and drug sensitivity databases predicted that the mechanistic target of rapamycin kinase (mTOR) and dual specificity mitogen-activated protein kinase kinase 2 (MAP2K2) represented potential therapeutic targets for the EMT and metabolism subtypes, respectively, and this was confirmed using selective inhibitors. Overall, our study provides novel, in-depth insights into GC proteomics, kinomics, and molecular taxonomy and reveals potential therapeutic targets that could provide the basis for precision treatments.
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Affiliation(s)
- Changyuan Hu
- Cancer Program, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
- Wenzhou Medical University‐Monash BDI Alliance in Clinical and Experimental BiomedicineWenzhou Medical UniversityChina
| | - Jiangning Song
- Cancer Program, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
| | - Terry Kwok
- Cancer Program, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
- Infection and Immunity Program, Monash Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
- Department of MicrobiologyMonash UniversityClaytonAustralia
| | - Elizabeth V. Nguyen
- Cancer Program, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
| | - Xian Shen
- Wenzhou Medical University‐Monash BDI Alliance in Clinical and Experimental BiomedicineWenzhou Medical UniversityChina
- Department of Gastrointestinal Surgery, The First Affiliated HospitalWenzhou Medical UniversityChina
| | - Roger J. Daly
- Cancer Program, Biomedicine Discovery InstituteMonash UniversityClaytonAustralia
- Department of Biochemistry and Molecular BiologyMonash UniversityClaytonAustralia
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Marzban H, Pedram N, Amini P, Gholampour Y, Saranjam N, Moradi S, Rahvarian J. Immunobiology of cancer stem cells and their immunoevasion mechanisms. Mol Biol Rep 2023; 50:9559-9573. [PMID: 37776412 DOI: 10.1007/s11033-023-08768-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 08/16/2023] [Indexed: 10/02/2023]
Abstract
Cancer stem cells (CSCs) defined as a small fraction of cells within malignancies have been isolated from tumors with different histological origins with stem related characteristics such as self-replicating potential, tumorigenesis, and therapy resistance. The dynamic communication between CSCs and tumor microenvironment particularly immune cells orchestrates their fate and plasticity as well as the patient outcome. According to recent evidence, it has been reported that they harness different immunological pathways to escape immunosurveillance and express aberrantly immunomodulatory agents or decreased levels of factors forming antigen presenting machinery (APM), subsequently followed by impaired antigen presentation and suppressed immune detection. As effective therapies are expected to be able to eradicate CSCs, mechanistic understanding of such interactions can provide insights into causes of therapy failure particularly in immunotherapy. Also, it can contribute to enhance the practical interventions against CSCs and their immunomodulatory features resulting in CSCs eradication and improving patient clinical outcome. The aim of this review is to explain the present knowledge regarding the immunobiology of CSCs and the immunoevasion mechanisms they use.
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Affiliation(s)
- Havva Marzban
- Department of Immunology, Mayo Clinic, Scottsdale, US.
| | - Nastaran Pedram
- Faculty of Veterinary Medicine, Department of Clinical Science, Shiraz University, Shiraz, Iran
| | - Parnian Amini
- Department of Veterinary Laboratory Science, Islamic Azad University, Rasht Branch, Rasht, Iran
| | - Yasaman Gholampour
- Faculty of Veterinary Medicine, Department of Clinical Sciences, Razi University, Kermanshah, Iran
| | | | - Samira Moradi
- Faculty of Medical Science, Department of Medicine, Hormozgan University, Bandar Abbas, Iran
| | - Jeiran Rahvarian
- Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Mashhad, Iran
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3
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He B, Gao R, Lv S, Chen A, Huang J, Wang L, Feng Y, Feng J, Liu B, Lei J, Deng B, He B, Cui B, Peng F, Yan M, Wang Z, Lam EWF, Jin B, Shao Z, Li Y, Jiao J, Wang X, Liu Q. Cancer cell employs a microenvironmental neural signal trans-activating nucleus-mitochondria coordination to acquire stemness. Signal Transduct Target Ther 2023; 8:275. [PMID: 37463926 PMCID: PMC10354099 DOI: 10.1038/s41392-023-01487-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 04/28/2023] [Accepted: 05/08/2023] [Indexed: 07/20/2023] Open
Abstract
Cancer cell receives extracellular signal inputs to obtain a stem-like status, yet how tumor microenvironmental (TME) neural signals steer cancer stemness to establish the hierarchical tumor architectures remains elusive. Here, a pan-cancer transcriptomic screening for 10852 samples of 33 TCGA cancer types reveals that cAMP-responsive element (CRE) transcription factors are convergent activators for cancer stemness. Deconvolution of transcriptomic profiles, specification of neural markers and illustration of norepinephrine dynamics uncover a bond between TME neural signals and cancer-cell CRE activity. Specifically, neural signal norepinephrine potentiates the stemness of proximal cancer cells by activating cAMP-CRE axis, where ATF1 serves as a conserved hub. Upon activation by norepinephrine, ATF1 potentiates cancer stemness by coordinated trans-activation of both nuclear pluripotency factors MYC/NANOG and mitochondrial biogenesis regulators NRF1/TFAM, thereby orchestrating nuclear reprograming and mitochondrial rejuvenating. Accordingly, single-cell transcriptomes confirm the coordinated activation of nuclear pluripotency with mitochondrial biogenesis in cancer stem-like cells. These findings elucidate that cancer cell acquires stemness via a norepinephrine-ATF1 driven nucleus-mitochondria collaborated program, suggesting a spatialized stemness acquisition by hijacking microenvironmental neural signals.
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Affiliation(s)
- Bin He
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Rui Gao
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
- Department of Medical Oncology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 510275, PR China
| | - Shasha Lv
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116023, PR China
| | - Ailin Chen
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Junxiu Huang
- Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, PR China
| | - Luoxuan Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116023, PR China
| | - Yunxiu Feng
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116023, PR China
| | - Jiesi Feng
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, 100871, PR China
| | - Bing Liu
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Jie Lei
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Bing Deng
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Bin He
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116023, PR China
| | - Bai Cui
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116023, PR China
| | - Fei Peng
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116023, PR China
| | - Min Yan
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Zifeng Wang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China
| | - Eric W-F Lam
- Department of Surgery and Cancer, Imperial College London, London, W12 0NN, UK
| | - Bilian Jin
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116023, PR China
| | - Zhiming Shao
- Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, 200032, PR China
| | - Yulong Li
- State Key Laboratory of Membrane Biology, Peking University School of Life Sciences, Beijing, 100871, PR China
| | - Jianwei Jiao
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, PR China
| | - Xi Wang
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China.
| | - Quentin Liu
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou, 510060, PR China.
- Department of Medical Oncology, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, 510275, PR China.
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, 116023, PR China.
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Ye J, Li P, Zhang H, Wu Q, Yang D. Identifying Prognostic Biomarkers Related to m6A Modification and Immune Infiltration in Renal Cell Carcinoma. Genes (Basel) 2022; 13:2059. [PMID: 36360294 PMCID: PMC9690957 DOI: 10.3390/genes13112059] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/02/2022] [Accepted: 11/04/2022] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Renal cell carcinoma (RCC) is the largest category of kidney tumors and usually does not have a good prognosis. N6-methyladenosine(m6A) and immune infiltration have received increased attention because of their great influence on the clinical outcome and prognosis of cancer patients. METHODS We identified hub genes through multi-dimensional screening, including DEGs, PPI analysis, LASSO regression, and random forest. Meanwhile, GO/KEGG enrichment, cMAP analysis, prognostic analysis, m6A prediction, and immune infiltration analysis were performed to understand the potential mechanism and screen therapeutic drugs. RESULTS We screened 275 downregulated and 185 upregulated genes using three GEO datasets and the TCGA dataset. In total, 82 candidate hub genes were selected using STRING and Cytoscape. Enrichment analysis illustrated that the top 3 biological process terms and top 1 KEGG term were related to immunity. cMAP analysis showed some antagonistic molecules can be candidate drugs for the treatment of RCC. Then, six hub genes (ERBB2, CASR, P2RY8, CAT, PLAUR, and TIMP1) with strong predictive values for prognosis and clinicopathological features were selected. Meanwhile, P2RY8, ERBB2, CAT, and TIMP1 may obtain m6A modification by binding METTL3 or METTL14. On the other hand, differential expression of CAT, ERBB2, P2RY8, PLAUR, and TIMP1 affects the infiltration of the majority of immune cells. CONCLUSIONS We identified six hub genes through multi-dimensional screening. They all possess strong predictive value for prognosis and clinicopathological features. Meanwhile, hub genes may regulate the progression of RCC via an m6A- and immunity-dependent mechanism.
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Affiliation(s)
- Junjie Ye
- The Second Affiliated Hospital of Soochow University, Suzhou 215000, China
- Lishui City People’s Hospital, Lishui 323000, China
| | - Peng Li
- Lishui City People’s Hospital, Lishui 323000, China
| | | | - Qi Wu
- Lishui City People’s Hospital, Lishui 323000, China
| | - Dongrong Yang
- The Second Affiliated Hospital of Soochow University, Suzhou 215000, China
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Johnson AL, Laterra J, Lopez-Bertoni H. Exploring glioblastoma stem cell heterogeneity: Immune microenvironment modulation and therapeutic opportunities. Front Oncol 2022; 12:995498. [PMID: 36212415 PMCID: PMC9532940 DOI: 10.3389/fonc.2022.995498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 09/02/2022] [Indexed: 11/29/2022] Open
Abstract
Despite its growing use in cancer treatment, immunotherapy has been virtually ineffective in clinical trials for gliomas. The inherently cold tumor immune microenvironment (TIME) in gliomas, characterized by a high ratio of pro-tumor to anti-tumor immune cell infiltrates, acts as a seemingly insurmountable barrier to immunotherapy. Glioma stem cells (GSCs) within these tumors are key contributors to this cold TIME, often functioning indirectly through activation and recruitment of pro-tumor immune cell types. Furthermore, drivers of GSC plasticity and heterogeneity (e.g., reprogramming transcription factors, epigenetic modifications) are associated with induction of immunosuppressive cell states. Recent studies have identified GSC-intrinsic mechanisms, including functional mimicry of immune suppressive cell types, as key determinants of anti-tumor immune escape. In this review, we cover recent advancements in our understanding of GSC-intrinsic mechanisms that modulate GSC-TIME interactions and discuss cutting-edge techniques and bioinformatics platforms available to study immune modulation at high cellular resolution with exploration of both malignant (i.e., GSC) and non-malignant (i.e., immune) cell fractions. Finally, we provide insight into the therapeutic opportunities for targeting immunomodulatory GSC-intrinsic mechanisms to potentiate immunotherapy response in gliomas.
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Affiliation(s)
- Amanda L. Johnson
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - John Laterra
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: John Laterra, ; Hernando Lopez-Bertoni,
| | - Hernando Lopez-Bertoni
- Hugo W. Moser Research Institute at Kennedy Krieger, Baltimore, MD, United States
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- *Correspondence: John Laterra, ; Hernando Lopez-Bertoni,
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