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Zhang G, Tai P, Fang J, Wang Z, Yu R, Yin Z, Cao K. Multi-omics reveals the impact of cancer-associated fibroblasts on the prognosis and treatment response of adult diffuse highest-grade gliomas. Heliyon 2024; 10:e34526. [PMID: 39157370 PMCID: PMC11327523 DOI: 10.1016/j.heliyon.2024.e34526] [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: 02/28/2024] [Revised: 07/09/2024] [Accepted: 07/10/2024] [Indexed: 08/20/2024] Open
Abstract
Background Cancer associated fibroblasts (CAF), an important cancer-promoting and immunosuppressive component of the tumor immune microenvironment (TIME), have recently been found to infiltrate adult diffuse highest-grade gliomas (ADHGG) (gliomas of grade IV). Methods Gene expression and clinical data of ADHGG patients were obtained from the CGGA and TCGA databases. Consensus clustering was used to identify CAF subtypes based on CAF key genes acquired from single-cell omics and spatial transcriptomomics. CIBERSORT, ssGSEA, MCPcounter, and ESTIMATE analyses were used to assess the TIME of GBM. Survival analysis, drug sensitivity analysis, TCIA database, TIDE and cMap algorithms were used to compare the prognosis and treatment response between patients with different CAF subtypes. An artificial neural network (ANN) model based on random forest was constructed to exactly identify CAF subtypes, which was validated in a real-world patient cohort of ADHGG. Results Consensus clustering classified ADHGG into two CAF subtypes. Compared with subtype B, patients with ADHGG subtype A had a poorer prognosis, worse responsiveness to immunotherapy and radiotherapy, higher CAF infiltration in TIME, but higher sensitivity to temozolomide. Furthermore, patients with subtype A had a much lower proportion of IDH mutations. Finally, the ANN model based on five genes (COL3A1, COL1A2, CD248, FN1, and COL1A1) could exactly discriminate CAF subtypes, and the validation of the real-world cohort indicated consistent results with the bioinformatics analyses. Conclusion This study revealed a novel CAF subtype to distinguish ADHGG patients with different prognosis and treatment responsiveness, which may be helpful for accurate clinical decision-making of ADHGG.
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Affiliation(s)
| | | | - Jianing Fang
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhanwang Wang
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Rui Yu
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhijing Yin
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Ke Cao
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China
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2
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Zhang S, Liu Y, Xie Y, Ding C, Zuo R, Guo Z, Qi S, Fu T, Chen W. Fe 3O 4@R837 Nanoplatform Enhances Chemical Dynamic Therapy and Immunotherapy: Integrated Transcriptomic Analysis Reveals Key Genes in Breast Cancer Prognosis. ACS Biomater Sci Eng 2024; 10:5274-5289. [PMID: 39056174 DOI: 10.1021/acsbiomaterials.4c00776] [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] [Indexed: 07/28/2024]
Abstract
Breast cancer represents a substantial contributor to mortality rates among women with cancer. Chemical dynamic therapy is a promising anticancer strategy that utilizes the Fenton reaction to transform naturally occurring hydrogen peroxide (H2O2) into hydroxyl radicals (•OH). Additionally, cancer immunotherapy using immune drugs, such as imiquimod (R837), has shown promise in activating T cells to kill tumor cells. In this study, we proposed a Fe3O4@R837 smart nanoplatform that can trigger the Fenton reaction and induce immune responses in breast cancer treatment. Furthermore, we performed transcriptome sequencing on breast cancer samples and used the R package (limma) to analyze differential expression profiles and select differentially expressed genes (DEGs). We obtained clinical information and RNA expression matrix data from The Cancer Genome Atlas database to perform survival analysis and identify prognostic-related genes (PRGs) and molecular subtypes with distinct prognoses. We used the TIMER 2.0 web and other methods to determine the tumor immune microenvironment and immune status of different prognostic subtypes. We identified DPGs by taking the intersection of DEGs and PRGs and performed functional analyses, including gene ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analysis, to elucidate potential mechanisms. Subsequently, we constructed a protein-protein interaction network using the STRING database to visualize the interactions between the DPGs. We screened hub genes from the DPGs using the Cytoscape plugin and identified six hub genes: CD3E, GZMK, CD27, SH2D1A, ZAP70, and TIGIT. Our results indicate that these six key genes regulate immune cell recruitment to increase T-cell cytotoxicity and kill tumors. Targeting these key genes can enhance immunotherapy and improve the breast cancer prognosis.
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Affiliation(s)
- Shichao Zhang
- Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361000, P. R. China
- The Second Hospital of Tianjin Medical University, Tianjin 300211, P. R. China
| | - Yijiang Liu
- First Affiliate Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361000, P. R. China
| | - Yuhan Xie
- The Second Hospital of Tianjin Medical University, Tianjin 300211, P. R. China
| | - Chenchun Ding
- Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361000, P. R. China
| | - Renjie Zuo
- Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361000, P. R. China
| | - Zhenzhen Guo
- School of Pharmaceutical Sciences, Xiamen University, Xiamen 361102, P. R. China
| | - Shiyong Qi
- The Second Hospital of Tianjin Medical University, Tianjin 300211, P. R. China
| | - Tingting Fu
- School of Basic Medical Science, Ningxia Medical University, Yinchuan 750004, P. R. China
| | - Weibin Chen
- Zhongshan Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen 361000, P. R. China
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3
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Zhao M, Wang L, Wang X, He J, Yu K, Li D. Non-neoplastic cells as prognostic biomarkers in diffuse large B-cell lymphoma: A system review and meta-analysis. TUMORI JOURNAL 2024; 110:227-240. [PMID: 38183180 DOI: 10.1177/03008916231221636] [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] [Indexed: 01/07/2024]
Abstract
The microenvironment of diffuse large B-cell lymphoma (DLBCL) is composed of various components, including immune cells and immune checkpoints, some of which have been correlated with the prognosis of DLBCL, but their results remain controversial. Therefore, we conducted a systematic review and meta-analysis to investigate the association between the microenvironment and prognosis in DLBCL. We searched PubMed, Web of Science, and EMBASE for relevant articles between 2001 and 2022. Twenty-five studies involving 4495 patients with DLBCL were included in the analysis. This meta-analysis confirmed that high densities of Foxp3+Tregs and PD-1+T cells are good indicators for overall survival (OS) in DLBCL, while high densities of programmed cell death protein ligand1(PD-L1)-positive expression cells and T-cell immunoglobulin-and mucin domain-3-containing molecule 3 (TIM-3)-positive expression tumor-infiltrating cells (TILs) play a contrary role in OS. Additionally, higher numbers of T-cell intracytoplasmic antigen-1(TIA-1)-positive expression T cells imply better OS and progression-free survival (PFS), while high numbers of lymphocyte activation gene(LAG)-positive expression TILs predict bad OS and PFS. Various non-tumoral cells in the microenvironment play important roles in the prognosis of DLBCL.
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MESH Headings
- Humans
- Lymphoma, Large B-Cell, Diffuse/pathology
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/metabolism
- Lymphoma, Large B-Cell, Diffuse/mortality
- Prognosis
- Tumor Microenvironment/immunology
- Biomarkers, Tumor/metabolism
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
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Affiliation(s)
- Min Zhao
- Department of Pathology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Pathology, Chongqing Medical University, Chongqing, China
- Molecular Medicine Diagnostic and Testing Center of Chongqing Medical University, Chongqing, China
| | - Lixing Wang
- Department of Pathology, Chongqing Medical University, Chongqing, China
| | - Xingyu Wang
- Department of Pathology, Chongqing Medical University, Chongqing, China
| | - Juan He
- Department of Pathology, Chongqing Medical University, Chongqing, China
| | - Kuai Yu
- Department of Pathology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Molecular Medicine Diagnostic and Testing Center of Chongqing Medical University, Chongqing, China
- Department of Pathology, Yongchuan Hospital of Chongqing Medical University, Chongqing, China
| | - Dan Li
- Department of Pathology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
- Department of Pathology, Chongqing Medical University, Chongqing, China
- Molecular Medicine Diagnostic and Testing Center of Chongqing Medical University, Chongqing, China
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4
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Harris MA, Savas P, Virassamy B, O'Malley MMR, Kay J, Mueller SN, Mackay LK, Salgado R, Loi S. Towards targeting the breast cancer immune microenvironment. Nat Rev Cancer 2024; 24:554-577. [PMID: 38969810 DOI: 10.1038/s41568-024-00714-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/31/2024] [Indexed: 07/07/2024]
Abstract
The tumour immune microenvironment is shaped by the crosstalk between cancer cells, immune cells, fibroblasts, endothelial cells and other stromal components. Although the immune tumour microenvironment (TME) serves as a source of therapeutic targets, it is also considered a friend or foe to tumour-directed therapies. This is readily illustrated by the importance of T cells in triple-negative breast cancer (TNBC), culminating in the advent of immune checkpoint therapy in combination with cytotoxic chemotherapy as standard of care for both early and advanced-stage TNBC, as well as recent promising signs of efficacy in a subset of hormone receptor-positive disease. In this Review, we discuss the various components of the immune TME in breast cancer and therapies that target or impact the immune TME, as well as the complexity of host physiology.
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Affiliation(s)
- Michael A Harris
- The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Peter Savas
- The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Balaji Virassamy
- The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Megan M R O'Malley
- The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Jasmine Kay
- The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, Victoria, Australia
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Scott N Mueller
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Laura K Mackay
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Parkville, Victoria, Australia
| | - Roberto Salgado
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Pathology, ZAS Ziekenhuizen, Antwerp, Belgium
| | - Sherene Loi
- The Sir Peter MacCallum Department of Medical Oncology, University of Melbourne, Melbourne, Victoria, Australia.
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.
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5
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Kader T, Provenzano E, Jayawardana MW, Hendry S, Pang JM, Elder K, Byrne DJ, Tjoeka L, Frazer HM, House E, Jayasinghe SI, Keane H, Murugasu A, Rajan N, Miligy IM, Toss M, Green AR, Rakha EA, Fox SB, Mann GB, Campbell IG, Gorringe KL. Stromal lymphocytes are associated with upgrade of B3 breast lesions. Breast Cancer Res 2024; 26:115. [PMID: 38978071 PMCID: PMC11232297 DOI: 10.1186/s13058-024-01857-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 06/10/2024] [Indexed: 07/10/2024] Open
Abstract
Various histopathological, clinical and imaging parameters have been evaluated to identify a subset of women diagnosed with lesions with uncertain malignant potential (B3 or BIRADS 3/4A lesions) who could safely be observed rather than being treated with surgical excision, with little impact on clinical practice. The primary reason for surgery is to rule out an upgrade to either ductal carcinoma in situ or invasive breast cancer, which occurs in up to 30% of patients. We hypothesised that the stromal immune microenvironment could indicate the presence of carcinoma associated with a ductal B3 lesion and that this could be detected in biopsies by counting lymphocytes as a predictive biomarker for upgrade. A higher number of lymphocytes in the surrounding specialised stroma was observed in upgraded ductal and papillary B3 lesions than non-upgraded (p < 0.01, negative binomial model, n = 307). We developed a model using lymphocytes combined with age and the type of lesion, which was predictive of upgrade with an area under the curve of 0.82 [95% confidence interval 0.77-0.87]. The model can identify some patients at risk of upgrade with high sensitivity, but with limited specificity. Assessing the tumour microenvironment including stromal lymphocytes may contribute to reducing unnecessary surgeries in the clinic, but additional predictive features are needed.
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MESH Headings
- Humans
- Female
- Breast Neoplasms/pathology
- Breast Neoplasms/immunology
- Tumor Microenvironment/immunology
- Middle Aged
- Aged
- Lymphocytes/immunology
- Lymphocytes/pathology
- Stromal Cells/pathology
- Adult
- Neoplasm Grading
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Carcinoma, Intraductal, Noninfiltrating/immunology
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Ductal, Breast/immunology
- Biomarkers, Tumor
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Affiliation(s)
- Tanjina Kader
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3010, Australia
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Elena Provenzano
- Department of Histopathology, Addenbrookes Hospital, and Cambridge NIH Biomedical Research Centre, Cambridge, UK
| | - Madawa W Jayawardana
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3010, Australia
| | - Shona Hendry
- Department of Anatomical Pathology, St Vincent's Hospital, Fitzroy, Australia
| | - Jia-Min Pang
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, 3000, Australia
| | - Kenneth Elder
- The Breast Service, The Royal Women's Hospital, Melbourne, Australia
- Edinburgh Breast Unit, Edinburgh, UK
| | - David J Byrne
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, 3000, Australia
| | - Lauren Tjoeka
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, 3000, Australia
| | - Helen Ml Frazer
- St Vincent's Breast Screen, St Vincent's Hospital Melbourne, Melbourne, VIC, Australia
- BreastScreen Victoria, Parkville, VIC, Australia
| | - Eloise House
- Department of Anatomical Pathology, St Vincent's Hospital, Fitzroy, Australia
| | - Sureshni I Jayasinghe
- Department of Anatomical Pathology, St Vincent's Hospital, Fitzroy, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, 3010, Australia
| | - Holly Keane
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, 3000, Australia
| | - Anand Murugasu
- The Breast Service, The Royal Women's Hospital, Melbourne, Australia
| | - Neeha Rajan
- The Breast Service, The Royal Women's Hospital, Melbourne, Australia
| | - Islam M Miligy
- Nottingham Breast Cancer Research Centre, Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, Department of Histopathology, University of Nottingham, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
- Histopathology Department, Faculty of Medicine, Menoufia University, Shibin El Kom, Egypt
| | - Michael Toss
- Nottingham Breast Cancer Research Centre, Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, Department of Histopathology, University of Nottingham, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
- Histopathology Department, Faculty of Medicine, Menoufia University, Shibin El Kom, Egypt
| | - Andrew R Green
- Nottingham Breast Cancer Research Centre, Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, Department of Histopathology, University of Nottingham, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
| | - Emad A Rakha
- Nottingham Breast Cancer Research Centre, Academic Unit for Translational Medical Sciences, School of Medicine, Biodiscovery Institute, Department of Histopathology, University of Nottingham, Nottingham University Hospitals NHS Trust, City Hospital, Nottingham, UK
- Pathology Department, Hamad Medical Corporation, Doha, Qatar
| | - Stephen B Fox
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, 3000, Australia
| | - G Bruce Mann
- The Royal Melbourne Hospital, Melbourne, Australia
- Department of Surgery, The University of Melbourne, Parkville, 3010, Australia
- The Breast Service, The Royal Women's Hospital, Melbourne, Australia
| | - Ian G Campbell
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, 3000, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3010, Australia
- Department of Clinical Pathology, The University of Melbourne, Parkville, 3010, Australia
| | - Kylie L Gorringe
- Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, 3000, Australia.
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, 3010, Australia.
- Department of Clinical Pathology, The University of Melbourne, Parkville, 3010, Australia.
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6
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Liu Z, Petinrin OO, Toseef M, Chen N, Wong KC. Construction of Immune Infiltration-Related LncRNA Signatures Based on Machine Learning for the Prognosis in Colon Cancer. Biochem Genet 2024; 62:1925-1952. [PMID: 37792224 DOI: 10.1007/s10528-023-10516-4] [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: 07/10/2023] [Accepted: 09/05/2023] [Indexed: 10/05/2023]
Abstract
Colon cancer is one of the malignant tumors with high morbidity, lethality, and prevalence across global human health. Molecular biomarkers play key roles in its prognosis. In particular, immune-related lncRNAs (IRL) have attracted enormous interest in diagnosis and treatment, but less is known about their potential functions. We aimed to investigate dysfunctional IRL and construct a risk model for improving the outcomes of patients. Nineteen immune cell types were collected for identifying house-keeping lncRNAs (HKLncRNA). GSE39582 and TCGA-COAD were treated as the discovery and validation datasets, respectively. Four machine learning algorithms (LASSO, Random Forest, Boruta, and Xgboost) and a Gaussian mixture model were utilized to mine the optimal combination of lncRNAs. Univariate and multivariate Cox regression was utilized to construct the risk score model. We distinguished the functional difference in an immune perspective between low- and high-risk cohorts calculated by this scoring system. Finally, we provided a nomogram. By leveraging the microarray, sequencing, and clinical data for immune cells and colon cancer patients, we identified the 221 HKLncRNAs with a low cell type-specificity index. Eighty-seven lncRNAs were up-regulated in the immune compared to cancer cells. Twelve lncRNAs were beneficial in improving performance. A risk score model with three lncRNAs (CYB561D2, LINC00638, and DANCR) was proposed with robust ROC performance on an independent dataset. According to immune-related analysis, the risk score is strongly associated with the tumor immune microenvironment. Our results emphasized IRL has the potential to be a powerful and effective therapy for enhancing the prognostic of colon cancer.
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Affiliation(s)
- Zhe Liu
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | | | - Muhammad Toseef
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Nanjun Chen
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Ka-Chun Wong
- Department of Computer Science, City University of Hong Kong, Hong Kong, China.
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7
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Cheng TYD, Fu DA, Falzarano SM, Zhang R, Datta S, Zhang W, Omilian AR, Aduse-Poku L, Bian J, Irianto J, Asirvatham JR, Campbell-Thompson M. Association of computed tomography scan-assessed body composition with immune and PI3K/AKT pathway proteins in distinct breast cancer tumor components. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.21.24307688. [PMID: 38826360 PMCID: PMC11142286 DOI: 10.1101/2024.05.21.24307688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
This hypothesis-generating study aims to examine the extent to which computed tomography-assessed body composition phenotypes are associated with immune and PI3K/AKT signaling pathways in breast tumors. A total of 52 patients with newly diagnosed breast cancer were classified into four body composition types: adequate (lowest two tertiles of total adipose tissue [TAT]) and highest two tertiles of total skeletal muscle [TSM] areas); high adiposity (highest tertile of TAT and highest two tertiles of TSM); low muscle (lowest tertile of TSM and lowest two tertiles of TAT); and high adiposity with low muscle (highest tertile of TAT and lowest tertile of TSM). Immune and PI3K/AKT pathway proteins were profiled in tumor epithelium and the leukocyte-enriched stromal microenvironment using GeoMx (NanoString). Linear mixed models were used to compare log2-transformed protein levels. Compared with the normal type, the low muscle type was associated with higher expression of INPP4B (log2-fold change = 1.14, p = 0.0003, false discovery rate = 0.028). Other significant associations included low muscle type with increased CTLA4 and decreased pan-AKT expression in tumor epithelium, and high adiposity with increased CD3, CD8, CD20, and CD45RO expression in stroma (P<0.05; false discovery rate >0.2). With confirmation, body composition can be associated with signaling pathways in distinct components of breast tumors, highlighting the potential utility of body composition in informing tumor biology and therapy efficacies.
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8
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Chen X, Zhang T, He YQ, Miao TW, Yin J, Ding Q, Yang M, Chen FY, Zeng HP, Liu J, Zhu Q. NGEF is a potential prognostic biomarker and could serve as an indicator for immunotherapy and chemotherapy in lung adenocarcinoma. BMC Pulm Med 2024; 24:248. [PMID: 38764064 PMCID: PMC11102621 DOI: 10.1186/s12890-024-03046-1] [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: 10/16/2023] [Accepted: 05/06/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND Neuronal guanine nucleotide exchange factor (NGEF) plays a key role in several cancers; however, its role in lung adenocarcinoma (LUAD) remains unclear. The aim of this study was to evaluate the efficacy of NGEF as a prognostic biomarker and potential therapeutic target for LUAD. METHODS NGEF expression data for multiple cancers and LUAD were downloaded from multiple databases. The high- and low-NGEF expression groups were constructed based on median NGEF expression in LUAD samples, and then performed Kaplan-Meier survival analysis. Differentially expressed genes (DEGs) from the two NGEF expression groups were screened and applied to construct a protein-protein interaction network. The primary pathways were obtained using gene set enrichment analysis. The associations between NGEF expression and clinical characteristics, immune infiltration, immune checkpoint inhibitors (ICIs), sensitivity to chemotherapy, and tumor mutation burden (TMB) were investigated using R. Levels of NGEF expression in the lung tissue was validated using single-cell RNA sequencing, quantitative polymerase chain reaction (qPCR), immunohistochemical staining, and western blot analysis. RESULTS The expression of NGEF mRNA was upregulated in multiple cancers. mRNA and protein expression levels of NGEF were higher in patients with LUAD than in controls, as validated using qPCR and western blot. High NGEF expression was an independent prognostic factor for LUAD and was associated with advanced tumor stage, large tumor size, more lymph node metastasis, and worse overall survival (OS). A total of 182 overlapping DEGs were screened between The Cancer Genome Atlas and GSE31210, among which the top 20 hub genes were identified. NGEF expression was mainly enriched in the pathways of apoptosis, cell cycle, and DNA replication. Moreover, elevated NGEF expression were associated with a high fraction of activated memory CD4+ T cells and M0 macrophages; elevated expression levels of the ICIs: programmed cell death 1 and programmed cell death 1 ligand 1 expression; higher TMB; and better sensitivity to bortezomib, docetaxel, paclitaxel, and parthenolide, but less sensitivity to axitinib and metformin. CONCLUSION NGEF expression is upregulated in LUAD and is significantly associated with tumor stages, OS probability, immune infiltration, immunotherapy response, and chemotherapy response. NGEF may be a potential diagnostic and prognostic biomarker and therapeutic target in LUAD.
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Affiliation(s)
- Xin Chen
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People's Hospital, Zigong, China.
| | - Tao Zhang
- Department of Intensive Care Unit, Chongqing General Hospital, University of Chinese Academy of Sciences, Chongqing, China
| | - Yan-Qiu He
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People's Hospital, Zigong, China
| | - Ti-Wei Miao
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People's Hospital, Zigong, China
| | - Jie Yin
- School of Automation & Information Engineering, Sichuan university of Science & Engineering, Zigong, China
| | - Qian Ding
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People's Hospital, Zigong, China
| | - Mei Yang
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People's Hospital, Zigong, China
| | - Fang-Ying Chen
- Department of Tuberculosis, The Third People's Hospital of Tibet Autonomous Region, Lhasa, China
| | - Hong-Ping Zeng
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People's Hospital, Zigong, China
| | - Jie Liu
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People's Hospital, Zigong, China
| | - Qi Zhu
- Department of Integrated Traditional Chinese and Western Medicine, Zigong First People's Hospital, Zigong, China
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9
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Lin S, Yong J, Zhang L, Chen X, Qiao L, Pan W, Yang Y, Zhao H. Applying image features of proximal paracancerous tissues in predicting prognosis of patients with hepatocellular carcinoma. Comput Biol Med 2024; 173:108365. [PMID: 38537563 DOI: 10.1016/j.compbiomed.2024.108365] [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: 10/18/2023] [Revised: 03/19/2024] [Accepted: 03/21/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Most of the methods using digital pathological image for predicting Hepatocellular carcinoma (HCC) prognosis have not considered paracancerous tissue microenvironment (PTME), which are potentially important for tumour initiation and metastasis. This study aimed to identify roles of image features of PTME in predicting prognosis and tumour recurrence of HCC patients. METHODS We collected whole slide images (WSIs) of 146 HCC patients from Sun Yat-sen Memorial Hospital (SYSM dataset). For each WSI, five types of regions of interests (ROIs) in PTME and tumours were manually annotated. These ROIs were used to construct a Lasso Cox survival model for predicting the prognosis of HCC patients. To make the model broadly useful, we established a deep learning method to automatically segment WSIs, and further used it to construct a prognosis prediction model. This model was tested by the samples of 225 HCC patients from the Cancer Genome Atlas Liver Hepatocellular Carcinoma (TCGA-LIHC). RESULTS In predicting prognosis of the HCC patients, using the image features of manually annotated ROIs in PTME achieved C-index 0.668 in the SYSM testing dataset, which is higher than the C-index 0.648 reached by the model only using image features of tumours. Integrating ROIs of PTME and tumours achieved C-index 0.693 in the SYSM testing dataset. The model using automatically segmented ROIs of PTME and tumours achieved C-index of 0.665 (95% CI: 0.556-0.774) in the TCGA-LIHC samples, which is better than the widely used methods, WSISA (0.567), DeepGraphSurv (0.593), and SeTranSurv (0.642). Finally, we found the Texture SumAverage Skew HV on immune cell infiltration and Texture related features on desmoplastic reaction are the most important features of PTME in predicting HCC prognosis. We additionally used the model in prediction HCC recurrence for patients from SYSM-training, SYSM-testing, and TCGA-LIHC datasets, indicating the important roles of PTME in the prediction. CONCLUSIONS Our results indicate image features of PTME is critical for improving the prognosis prediction of HCC. Moreover, the image features related with immune cell infiltration and desmoplastic reaction of PTME are the most important factors associated with prognosis of HCC.
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Affiliation(s)
- Siying Lin
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China; Department of Pathology, Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Juanjuan Yong
- Department of Pathology, Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China
| | - Lei Zhang
- Department of Pancreatic-Hepato-Biliary-Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
| | - Xiaolong Chen
- Department of Hepatic Surgery, Liver Transplantation, The Third Affiliated Hospital of Sun Yat-Sen University, Guangzhou, 510630, China
| | - Liang Qiao
- Storr Liver Centre, Westmead Institute for Medical Research, University of Sydney at Westmead Hospital, Westmead, NSW, 2145, Australia
| | - Weidong Pan
- Department of Pancreatic-Hepato-Biliary-Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, 510655, China
| | - Yuedong Yang
- School of Computer Science and Engineering, Sun Yat-sen University, Guangzhou, 510006, China.
| | - Huiying Zhao
- Department of Pathology, Department of Medical Research Center, Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, 510120, China.
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10
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Xu J, Zhang Y, Li M, Shao Z, Dong Y, Li Q, Bai H, Duan J, Zhong J, Wan R, Bai J, Yi X, Tang F, Wang J, Wang Z. A single-cell characterised signature integrating heterogeneity and microenvironment of lung adenocarcinoma for prognostic stratification. EBioMedicine 2024; 102:105092. [PMID: 38547579 PMCID: PMC10990706 DOI: 10.1016/j.ebiom.2024.105092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/15/2024] [Accepted: 03/15/2024] [Indexed: 04/07/2024] Open
Abstract
BACKGROUND The high heterogeneity of tumour and the complexity of tumour microenvironment (TME) greatly impacted the tumour development and the prognosis of cancer in the era of immunotherapy. In this study, we aimed to portray the single cell-characterised landscape of lung adenocarcinoma (LUAD), and develop an integrated signature incorporating both tumour heterogeneity and TME for prognosis stratification. METHODS Single-cell tagged reverse transcription sequencing (STRT-seq) was performed on tumour tissues and matched normal tissues from 14 patients with LUAD for immune landscape depiction and candidate key genes selection for signature construction. Kaplan-Meier survival analyses and in-vitro cell experiments were conducted to confirm the gene functions. The transcriptomic profile of 1949 patients from 11 independent cohorts including nine public datasets and two in-house cohorts were obtained for validation. FINDINGS We selected 11 key genes closely related to cell-to-cell interaction, tumour development, T cell phenotype transformation, and Ma/Mo cell distribution, including HLA-DPB1, FAM83A, ITGB4, OAS1, FHL2, S100P, FSCN1, SFTPD, SPP1, DBH-AS1, CST3, and established an integrated 11-gene signature, stratifying patients to High-Score or Low-Score group for better or worse prognosis. Moreover, the prognostically-predictive potency of the signature was validated by 11 independent cohorts, and the immunotherapeutic predictive potency was also validated by our in-house cohort treated by immunotherapy. Additionally, the in-vitro cell experiments and drug sensitivity prediction further confirmed the gene function and generalizability of this signature across the entire RNA profile spectrum. INTERPRETATION This single cell-characterised 11-gene signature might offer insights for prognosis stratification and potential guidance for treatment selection. FUNDING Support for the study was provided by National key research and development project (2022YFC2505004, 2022YFC2505000 to Z.W. and J.W.), Beijing Natural Science Foundation (7242114 to J.X.), National Natural Science Foundation of China of China (82102886 to J.X., 81871889 and 82072586 to Z.W.), Beijing Nova Program (20220484119 to J.X.), NSFC general program (82272796 to J.W.), NSFC special program (82241229 to J.W.), CAMS Innovation Fund for Medical Sciences (2021-1-I2M-012, 2022-I2M-1-009 to Z.W. and J.W.), Beijing Natural Science Foundation (7212084 to Z.W.), CAMS Key lab of translational research on lung cancer (2018PT31035 to J.W.), Aiyou Foundation (KY201701 to J.W.). Medical Oncology Key Foundation of Cancer Hospital Chinese Academy of Medical Sciences (CICAMS-MOCP2022003 to J.X.).
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Affiliation(s)
- Jiachen Xu
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yundi Zhang
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Man Li
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhuo Shao
- Geneplus-Beijing Institute, Changping District, Beijing, China
| | - Yiting Dong
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qingqing Li
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China; Beijing Advanced Innovation Center for Genomics & Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Hua Bai
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jianchun Duan
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Department of Medical Oncology, Shanxi Province Cancer Hospital/Shanxi Hospital Affiliated to Cancer Hospital, Chinese Academy of Medical Sciences/Cancer Hospital Affiliated to Shanxi Medical University, Taiyuan, China
| | - Jia Zhong
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Rui Wan
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jing Bai
- Geneplus-Beijing Institute, Changping District, Beijing, China
| | - Xin Yi
- Geneplus-Beijing Institute, Changping District, Beijing, China
| | - Fuchou Tang
- Biomedical Pioneering Innovation Center, School of Life Sciences, Peking University, Beijing, China; Beijing Advanced Innovation Center for Genomics & Ministry of Education Key Laboratory of Cell Proliferation and Differentiation, Beijing, China
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, CAMS Key Laboratory of Translational Research on Lung Cancer, Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
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11
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Sheva K, Roy Chowdhury S, Kravchenko-Balasha N, Meirovitz A. Molecular Changes in Breast Cancer Induced by Radiation Therapy. Int J Radiat Oncol Biol Phys 2024:S0360-3016(24)00435-8. [PMID: 38508467 DOI: 10.1016/j.ijrobp.2024.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 02/29/2024] [Accepted: 03/10/2024] [Indexed: 03/22/2024]
Abstract
PURPOSE Breast cancer treatments are based on prognostic clinicopathologic features that form the basis for therapeutic guidelines. Although the utilization of these guidelines has decreased breast cancer-associated mortality rates over the past three decades, they are not adequate for individualized therapy. Radiation therapy (RT) is the backbone of breast cancer treatment. Although a highly successful therapeutic modality clinically, from a biological perspective, preclinical studies have shown RT to have the potential to alter tumor cell phenotype, immunogenicity, and the surrounding microenvironment, potentially changing the behavior of cancer cells and resulting in a significant variation in RT response. This review presents the recent advances in revealing the complex molecular changes induced by RT in the treatment of breast cancer and highlights the complexities of translating this information into clinically relevant tools for improved prognostic insights and the revelation of novel approaches for optimizing RT. METHODS AND MATERIALS Current literature was reviewed with a focus on recent advances made in the elucidation of tumor-associated radiation-induced molecular changes across molecular, genetic, and proteomic bases. This review was structured with the aim of providing an up-to-date overview over the very broad and complex subject matter of radiation-induced molecular changes and radioresistance, familiarizing the reader with the broader issue at hand. RESULTS The subject of radiation-induced molecular changes in breast cancer has been broached from various physiological focal points including that of the immune system, immunogenicity and the abscopal effect, tumor hypoxia, breast cancer classification and subtyping, molecular heterogeneity, and molecular plasticity. It is becoming increasingly apparent that breast cancer clinical subtyping alone does not adequately account for variation in RT response or radioresistance. Multiple components of the tumor microenvironment and immune system, delivered RT dose and fractionation schedules, radiation-induced bystander effects, and intrinsic tumor physiology and heterogeneity all contribute to the resultant RT outcome. CONCLUSIONS Despite recent advances and improvements in anticancer therapies, tumor resistance remains a significant challenge. As new analytical techniques and technologies continue to provide crucial insight into the complex molecular mechanisms of breast cancer and its treatment responses, it is becoming more evident that personalized anticancer treatment regimens may be vital in overcoming radioresistance.
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Affiliation(s)
- Kim Sheva
- The Legacy Heritage Oncology Center & Dr Larry Norton Institute, Soroka University Medical Center, Ben Gurion University of the Negev, Faculty of Medicine, Be'er Sheva, Israel.
| | - Sangita Roy Chowdhury
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Nataly Kravchenko-Balasha
- The Institute of Biomedical and Oral Research, The Hebrew University of Jerusalem, Jerusalem, Israel.
| | - Amichay Meirovitz
- The Legacy Heritage Oncology Center & Dr Larry Norton Institute, Soroka University Medical Center, Ben Gurion University of the Negev, Faculty of Medicine, Be'er Sheva, Israel.
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12
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Wang P, Wang Y, Li H, Wang M, Wang Y, Wang X, Ran L, Xin H, Ma J, Tian G, Gao W, Zhang G. A homologous-targeting cGAS-STING agonist multimodally activates dendritic cells for enhanced cancer immunotherapy. Acta Biomater 2024; 177:400-413. [PMID: 38336268 DOI: 10.1016/j.actbio.2024.02.003] [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: 10/19/2023] [Revised: 01/27/2024] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Herein, we developed a doxorubicin (Dox)-loaded and 4T1 cancer cell membrane-modified hydrogenated manganese oxide nanoparticles (mHMnO-Dox) to elicit systemic antitumor immune responses. The results revealed that mHMnO-Dox actively recognized tumor cells and then effectively delivered Dox into the cells. Upon entering tumor cells, the mHMnO-Dox underwent rapid degradation and abundant release of Mn2+ and chemotherapeutic drugs. The released Mn2+ not only catalysed a Fenton-type reaction to produce excessive reactive oxygen species (ROS) but also activated the cGAS-STING pathway to boost dendritic cell (DC) maturation. This process increased cytotoxic T lymphocyte infiltration as well as natural killer cell recruitment into the tumor site. In addition, the released Dox could contribute to a chemotherapeutic effect, while activating DC cells and subsequently intensifying immune responses through immunogenic cell death (ICD) of tumor cells. Consequently, the mHMnO-Dox suppressed the primary and distal tumor growth and inhibited tumor relapse and metastasis, as well as prolonged the lifespan of tumor-bearing mice. Thus, the mHMnO-Dox multimodally activated DC cells to demonstrate synergistic antitumor activity, which was mediated via the activation of the cGAS-STING signalling pathway to regulate tumor microenvironment, ICD-mediated immunotherapy and ROS-mediated CDT. These findings suggest the therapeutic potential of mHMnO-Dox in cancer immunotherapy. STATEMENT OF SIGNIFICANCE: A cancer cell membrane-camouflaged hydrogenated mesoporous manganese oxide (mHMnO) has been developed as a cGAS-STING agonist and ICD inducer. The mHMnO effectively induced abundance of ROS production in cancer cells, which caused cancer cell death and then promoted DC maturation via tumour-associated antigen presentation. Meanwhile, the mHMnO significantly activated cGAS-STING pathway to facilitate DC maturation and cytotoxic T lymphocyte infiltration as well as natural killer cell recruitment, which further enhanced tumour immune response. In addition, the combination of the mHMnO and Dox could synergistically promote tumour ICD and then multimodally induce DC maturation, achieving an enhanced CIT. Overall, this study provides a potential strategy to design novel immunologic adjuvant for enhanced CIT.
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Affiliation(s)
- Peng Wang
- School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai 264003, PR China
| | - Yinfeng Wang
- School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai 264003, PR China
| | - Huimin Li
- School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai 264003, PR China
| | - Miaomiao Wang
- School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai 264003, PR China
| | - Yue Wang
- School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai 264003, PR China
| | - Xiaofei Wang
- School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai 264003, PR China
| | - Lang Ran
- School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai 264003, PR China
| | - Huan Xin
- School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai 264003, PR China
| | - Jingyi Ma
- School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai 264003, PR China
| | - Geng Tian
- School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai 264003, PR China
| | - Wenjuan Gao
- School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai 264003, PR China.
| | - Guilong Zhang
- School of Pharmacy, Shandong Technology Innovation Center of Molecular Targeting and Intelligent Diagnosis and Treatment, Binzhou Medical University, Yantai 264003, PR China.
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13
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Lin W, Yang H, Lin J, Yang X, Liao Z, Zheng Y, Luo P, Liu C. OralExplorer: a web server for exploring the mechanisms of oral inflammatory diseases. J Transl Med 2024; 22:282. [PMID: 38491529 PMCID: PMC10943789 DOI: 10.1186/s12967-024-05019-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 02/22/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Oral inflammatory diseases are localized infectious diseases primarily caused by oral pathogens with the potential for serious systemic complications. However, publicly available datasets for these diseases are underutilized. To address this issue, a web tool called OralExplorer was developed. This tool integrates the available data and provides comprehensive online bioinformatic analysis. METHODS Human oral inflammatory disease-related datasets were obtained from the GEO database and normalized using a standardized process. Transcriptome data were then subjected to differential gene expression analysis, immune infiltration analysis, correlation analysis, pathway enrichment analysis, and visualization. The single-cell sequencing data was visualized as cluster plot, feature plot, and heatmaps. The web platform was primarily built using Shiny. The biomarkers identified in OralExplorer were validated using local clinical samples through qPCR and IHC. RESULTS A total of 35 human oral inflammatory disease-related datasets, covering 6 main disease types and 901 samples, were included in the study to identify potential molecular signatures of the mechanisms of oral diseases. OralExplorer consists of 5 main analysis modules (differential gene expression analysis, immune infiltration analysis, correlation analysis, pathway enrichment analysis and single-cell analysis), with multiple visualization options. The platform offers a simple and intuitive interface, high-quality images for visualization, and detailed analysis results tables for easy access by users. Six markers (IL1β, SRGN, CXCR1, FGR, ARHGEF2, and PTAFR) were identified by OralExplorer. qPCR- and IHC-based experimental validation showed significantly higher levels of these genes in the periodontitis group. CONCLUSIONS OralExplorer is a comprehensive analytical platform for oral inflammatory diseases. It allows users to interactively explore the molecular mechanisms underlying the action and regression of these diseases. It also aids dental researchers in unlocking the potential value of transcriptomics data related to oral diseases. OralExplorer can be accessed at https://smuonco.shinyapps.io/OralExplorer/ (Alternate URL: http://robinl-lab.com/OralExplorer ).
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Affiliation(s)
- Weiyin Lin
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Hong Yang
- The Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Jiayu Lin
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Xia Yang
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Zhihao Liao
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Yifan Zheng
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China
| | - Peng Luo
- The Department of Oncology, Zhujiang Hospital, Southern Medical University, Guangzhou, China.
| | - Chufeng Liu
- Stomatological Hospital, School of Stomatology, Southern Medical University, Guangzhou, China.
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Chan R, Aphivatanasiri C, Poon IK, Tsang JY, Ni Y, Lacambra M, Li J, Lee C, Tse GM. Spatial Distribution and Densities of CD103+ and FoxP3+ Tumor Infiltrating Lymphocytes by Digital Analysis for Outcome Prediction in Breast Cancer. Oncologist 2024; 29:e299-e308. [PMID: 37491001 PMCID: PMC10911924 DOI: 10.1093/oncolo/oyad199] [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: 12/31/2022] [Accepted: 05/23/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND The evaluation of tumor-infiltrating lymphocytes (TILs) for breast cancer prognosis is now established. However, the clinical value for their spatial distributions of specific immune subsets, namely CD103+ tissue-resident memory T cells FoxP3+ regulatory T ells, have not been thoroughly examined. METHOD Representative whole sections of breast cancers were subjected to CD103 and FoxP3 double staining. Their density, ratio, and spatial features were analyzed in tumor area and tumor-stromal interface. Their associations with clinicopathological parameters and patient's prognosis were analyzed. RESULTS CD103 TILs were closer to tumor nests than FoxP3 TILs in the tumor-stromal interface. Their densities were associated with high-grade disease, TNBC, and stromal TILs. High stromal FoxP3 (sFoxP3) TILs and close proximity of sCD103 TILs to tumor were independently associated with better survival at multivariate analysis. Subgroup analysis showed the high FoxP3 TILs density associated better survival was seen in HER2-OE and TNBC subtypes while the proximity of CD103 TILs to tumor nests associated better survival was seen in luminal cancers. CONCLUSION The prognostic impact of CD103 and FoxP3 TILs in breast cancer depends on their spatial localization. High sFoxP3 TIL density and the lower distance of CD103 TILs from the tumor nests had independent favorable prognostic values.
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Affiliation(s)
- Ronald Chan
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Ngan Shing Street, Shatin, NT, Hong Kong
| | | | - Ivan K Poon
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Ngan Shing Street, Shatin, NT, Hong Kong
| | - Julia Y Tsang
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Ngan Shing Street, Shatin, NT, Hong Kong
| | - Yunbi Ni
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Ngan Shing Street, Shatin, NT, Hong Kong
| | - Maribel Lacambra
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Ngan Shing Street, Shatin, NT, Hong Kong
| | - Joshua Li
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Ngan Shing Street, Shatin, NT, Hong Kong
| | - Conrad Lee
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Ngan Shing Street, Shatin, NT, Hong Kong
| | - Gary M Tse
- Department of Anatomical and Cellular Pathology, State Key Laboratory of Translational Oncology, Prince of Wales Hospital, The Chinese University of Hong Kong, Ngan Shing Street, Shatin, NT, Hong Kong
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15
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Nicolini A, Ferrari P, Silvestri R, Gemignani F. The breast cancer tumor microenvironment and precision medicine: immunogenicity and conditions favoring response to immunotherapy. JOURNAL OF THE NATIONAL CANCER CENTER 2024; 4:14-24. [PMID: 39036381 PMCID: PMC11256721 DOI: 10.1016/j.jncc.2024.01.004] [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: 11/21/2023] [Revised: 01/13/2024] [Accepted: 01/21/2024] [Indexed: 07/23/2024] Open
Abstract
Some main recent researches that have dissected tumor microenvironment (TME) by imaging mass cytometry (IMC) in different subtypes of primary breast cancer samples were considered. The many phenotypic variants, clusters of epithelial tumor and immune cells, their structural features as well as the main genetic aberrations, sub-clonal heterogeneity and their systematic classification also have been examined. Mutational evolution has been assessed in primary and metastatic breast cancer samples. Overall, based on these findings the current concept of precision medicine is questioned and challenged by alternative therapeutic strategies. In the last two decades, immunotherapy as a powerful and harmless tool to fight cancer has received huge attention. Thus, the tumor immune microenvironment (TIME) composition, its prognostic role for clinical course as well as a novel definition of immunogenicity in breast cancer are proposed. Investigational clinical trials carried out by us and other findings suggest that G0-G1 state induced in endocrine-dependent metastatic breast cancer is more suitable for successful immune manipulation. Residual micro-metastatic disease seems to be another specific condition that can significantly favor the immune response in breast and other solid tumors.
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Affiliation(s)
- Andrea Nicolini
- Department of Oncology, Transplantations and New Technologies in Medicine, University of Pisa, Pisa, Italy
| | - Paola Ferrari
- Department of Oncology, Transplantations and New Technologies in Medicine, University of Pisa, Pisa, Italy
| | - Roberto Silvestri
- Department of Biology, Genetic Unit, University of Pisa, Pisa, Italy
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Alaluf E, Shalamov MM, Sonnenblick A. Update on current and new potential immunotherapies in breast cancer, from bench to bedside. Front Immunol 2024; 15:1287824. [PMID: 38433837 PMCID: PMC10905744 DOI: 10.3389/fimmu.2024.1287824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 01/12/2024] [Indexed: 03/05/2024] Open
Abstract
Impressive advances have been seen in cancer immunotherapy during the last years. Although breast cancer (BC) has been long considered as non-immunogenic, immunotherapy for the treatment of BC is now emerging as a new promising therapeutic approach with considerable potential. This is supported by a plethora of completed and ongoing preclinical and clinical studies in various types of immunotherapies. However, a significant gap between clinical oncology and basic cancer research impairs the understanding of cancer immunology and immunotherapy, hampering cancer therapy research and development. To exploit the accumulating available data in an optimal way, both fundamental mechanisms at play in BC immunotherapy and its clinical pitfalls must be integrated. Then, clinical trials must be critically designed with appropriate combinations of conventional and immunotherapeutic strategies. While there is room for major improvement, this updated review details the immunotherapeutic tools available to date, from bench to bedside, in the hope that this will lead to rethinking and optimizing standards of care for BC patients.
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Affiliation(s)
- Emmanuelle Alaluf
- Medical Oncology Clinic, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | | | - Amir Sonnenblick
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
- Oncology Division, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel
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17
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Said SS, Ibrahim WN. Breaking Barriers: The Promise and Challenges of Immune Checkpoint Inhibitors in Triple-Negative Breast Cancer. Biomedicines 2024; 12:369. [PMID: 38397971 PMCID: PMC10886684 DOI: 10.3390/biomedicines12020369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/06/2024] [Accepted: 01/08/2024] [Indexed: 02/25/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly aggressive malignancy with pronounced immunogenicity, exhibiting rapid proliferation and immune cell infiltration into the tumor microenvironment. TNBC's heterogeneity poses challenges to immunological treatments, inducing resistance mechanisms in the tumor microenvironment. Therapeutic modalities, including immune checkpoint inhibitors (ICIs) targeting PD-1, PD-L1, and CTLA-4, are explored in preclinical and clinical trials. Promising results emerge from combining ICIs with anti-TGF-β and VISTA, hindering TNBC tumor growth. TNBC cells employ complex evasion strategies involving interactions with stromal and immune cells, suppressing immune recognition through various cytokines, chemokines, and metabolites. The recent focus on unraveling humoral and cellular components aims to disrupt cancer crosstalk within the tumor microenvironment. This review identifies TNBC's latest resistance mechanisms, exploring potential targets for clinical trials to overcome immune checkpoint resistance and enhance patient survival rates.
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Affiliation(s)
| | - Wisam Nabeel Ibrahim
- Department of Biomedical Sciences, College of Health Sciences, QU Health, Qatar University, Doha P.O. Box 2713, Qatar;
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18
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Jääskeläinen MM, Tumelius R, Hämäläinen K, Rilla K, Oikari S, Rönkä A, Selander T, Mannermaa A, Tiainen S, Auvinen P. High Numbers of CD163+ Tumor-Associated Macrophages Predict Poor Prognosis in HER2+ Breast Cancer. Cancers (Basel) 2024; 16:634. [PMID: 38339385 PMCID: PMC10854814 DOI: 10.3390/cancers16030634] [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: 12/28/2023] [Revised: 01/22/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Tumor-associated macrophages (TAMs) are associated with a poor outcome in breast cancer (BC), but their prognostic value in different BC subtypes has remained somewhat unclear. Here, we investigated the prognostic value of M2-like TAMs (CD163+) and all TAMs (CD68+) in a patient cohort of 278 non-metastatic BC patients, half of whom were HER2+ (n = 139). The survival endpoints investigated were overall survival (OS), breast cancer-specific survival (BCSS) and disease-free survival (DFS). In the whole patient cohort (n = 278), a high CD163+ TAM count and a high CD68+ TAM count were associated with a worse outcome (p ≤ 0.023). In HER2+ BC, a high CD163+ TAM count was an independent factor for a poor prognosis across all the investigated survival endpoints (p < 0.001). The prognostic effect was evident in both the HER2+/hormone receptor-positive (p < 0.001) and HER2+/hormone receptor-negative (p ≤ 0.012) subgroups and regardless of the provision of adjuvant trastuzumab (p ≤ 0.002). In HER2-negative BC, the CD163+ TAM count was not significantly associated with survival. These results suggest that a high CD163+ TAM count predicts an inferior outcome, especially in HER2+ BC patients, and as adjuvant trastuzumab did not overcome the poor prognostic effect, combination treatments including therapies targeting the macrophage function could represent an effective therapeutic approach in HER2+ BC.
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Affiliation(s)
- Minna M. Jääskeläinen
- Cancer Center, Kuopio University Hospital, Wellbeing Services County of North Savo, 70029 Kuopio, Finland
- Institute of Clinical Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Ritva Tumelius
- Kuopio Center for Gene and Cell Therapy, 70210 Kuopio, Finland
| | - Kirsi Hämäläinen
- Institute of Clinical Medicine, Clinical Pathology and Forensic Medicine, University of Eastern Finland, 70211 Kuopio, Finland
- Imaging Center, Clinical Pathology, Kuopio University Hospital, Wellbeing Services County of North Savo, 70029 Kuopio, Finland
- Biocenter Kuopio and Cancer Center of Eastern Finland, University of Eastern Finland, 70211 Kuopio, Finland
| | - Kirsi Rilla
- Institute of Biomedicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Sanna Oikari
- Institute of Biomedicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Aino Rönkä
- Cancer Center, Kuopio University Hospital, Wellbeing Services County of North Savo, 70029 Kuopio, Finland
- Institute of Clinical Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Tuomas Selander
- Science Services Center, Kuopio University Hospital, Wellbeing Services County of North Savo, 70029 Kuopio, Finland
| | - Arto Mannermaa
- Institute of Clinical Medicine, Clinical Pathology and Forensic Medicine, University of Eastern Finland, 70211 Kuopio, Finland
- Biobank of Eastern Finland, Kuopio University Hospital, Wellbeing Services County of North Savo, 700029 Kuopio, Finland
| | - Satu Tiainen
- Cancer Center, Kuopio University Hospital, Wellbeing Services County of North Savo, 70029 Kuopio, Finland
- Institute of Clinical Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Päivi Auvinen
- Cancer Center, Kuopio University Hospital, Wellbeing Services County of North Savo, 70029 Kuopio, Finland
- Institute of Clinical Medicine, University of Eastern Finland, 70211 Kuopio, Finland
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Quail DF, Park M, Welm AL, Ekiz HA. Breast Cancer Immunity: It is TIME for the Next Chapter. Cold Spring Harb Perspect Med 2024; 14:a041324. [PMID: 37188526 PMCID: PMC10835621 DOI: 10.1101/cshperspect.a041324] [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: 05/17/2023]
Abstract
Our ability to interrogate the tumor immune microenvironment (TIME) at an ever-increasing granularity has uncovered critical determinants of disease progression. Not only do we now have a better understanding of the immune response in breast cancer, but it is becoming possible to leverage key mechanisms to effectively combat this disease. Almost every component of the immune system plays a role in enabling or inhibiting breast tumor growth. Building on early seminal work showing the involvement of T cells and macrophages in controlling breast cancer progression and metastasis, single-cell genomics and spatial proteomics approaches have recently expanded our view of the TIME. In this article, we provide a detailed description of the immune response against breast cancer and examine its heterogeneity in disease subtypes. We discuss preclinical models that enable dissecting the mechanisms responsible for tumor clearance or immune evasion and draw parallels and distinctions between human disease and murine counterparts. Last, as the cancer immunology field is moving toward the analysis of the TIME at the cellular and spatial levels, we highlight key studies that revealed previously unappreciated complexity in breast cancer using these technologies. Taken together, this article summarizes what is known in breast cancer immunology through the lens of translational research and identifies future directions to improve clinical outcomes.
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Affiliation(s)
- Daniela F Quail
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec H3A 1A3, Canada
- Department of Physiology, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Morag Park
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, Quebec H3A 1A3, Canada
- Departments of Biochemistry, Oncology, McGill University, Montreal, Quebec H3G 1Y6, Canada
| | - Alana L Welm
- Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - H Atakan Ekiz
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Gulbahce, 35430 Urla, Izmir, Turkey
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20
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He Z, Chen M, Luo Z. Identification of immune-related genes and integrated analysis of immune-cell infiltration in melanoma. Aging (Albany NY) 2024; 16:911-927. [PMID: 38217549 PMCID: PMC10817386 DOI: 10.18632/aging.205427] [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: 09/13/2023] [Accepted: 12/04/2023] [Indexed: 01/15/2024]
Abstract
OBJECTIVE This study was conducted to screen out immune-related genes in connection with the prognosis of melanoma, construct a prognosis model and explore the relevant mechanisms. METHODS AND MATERIALS 1973 genes associated with immune system were derived from the Immport database, and RNA-seq data of melanoma and information of patients were searched from the Xena database. Cox univariate analysis, Lasso analysis and Cox multivariate analysis were used to screen out six genes to construct the model. Then the risk scores were estimated for patients based on our constructed prognosis model. Estimate was used to affirm that the model was about immune infiltration, and CIBERSORT was used to screen out immune cells associated with prognosis. TIDE was applied to predict the efficacy of immunotherapy. Finally, GSE65904 and GSE19234 were used to confirm the effectiveness of the model. RESULTS ADCYAP1R1, GPI, NTS might cause poor prognosis while IFITM1, KIR2DL4, LIF were more likely conductive to prognosis of melanoma patients and a model of prognosis was constructed on the basis of these six genes. The effectiveness of the model has been proven by the ROC curve, and the miRNAs targeting the screened genes were found out, suggesting that the immune system might impact on the prognosis of melanoma by T cell CD8+, T cell CD4+ memory and NK cells. CONCLUSIONS In this study, the screened six genes were associated with the prognosis of melanoma, which was conductive to clinical prognostic prediction and individualized treatment strategy.
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Affiliation(s)
- Zhenghao He
- Department of Plastic Surgery, Zhongshan City People's Hospital, Zhongshan 528403, Guangdong, China
| | - Manli Chen
- Department of Plastic Surgery, Zhongshan City People's Hospital, Zhongshan 528403, Guangdong, China
| | - Zhijun Luo
- Department of Plastic Surgery, Zhongshan City People's Hospital, Zhongshan 528403, Guangdong, China
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21
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Li Y, Liang X, Li H, Chen X. Reconstruction of unreported subgroup survival data with PD-L1-low expression in advanced/metastatic triple-negative breast cancer using innovative KMSubtraction workflow. J Immunother Cancer 2024; 12:e007931. [PMID: 38212119 PMCID: PMC10806559 DOI: 10.1136/jitc-2023-007931] [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: 12/13/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Among patients with advanced/metastatic triple-negative breast cancer (TNBC) with high/positive programmed death-ligand 1 (PD-L1) expression, a superior survival outcome has been demonstrated with immune checkpoint inhibitors (ICIs). However, it remains unclear whether ICIs are beneficial for patients with low PD-L1 levels. Here, we derived survival data for subgroups with low PD-L1-expressing and conducted a pooled analysis. METHODS After a systematic search of Embase, PubMed, MEDLINE, and CENTRAL from inception until May 18, 2023, randomized controlled trials (RCTs) reporting progression-free survival (PFS), overall survival (OS), or duration of response (DOR) for metastatic TNBC treated with ICI-based regimens were included. Kaplan-Meier curves were extracted for the intention-to-treat population and high PD-L1 subgroups. KMSubtraction was used when survival curves were not provided for subgroups with low PD-L1 expression. A pooled analysis of survival data was then conducted. RESULTS A total of 3022 patients were included in four RCTs: Impassion130, Impassion131, KEYNOTE-119, and KEYNOTE-355. Unreported low PD-L1-expressing subgroups were identified, including PD-L1 immune cell (IC)<1%, combined positive score (CPS)<1, and 1≤CPS<10. Compared with chemotherapy, ICI-chemotherapy combinations did not significantly differ in OS, PFS, or DOR in the Impassion PD-L1<1%, KEYNOTE-355 PD-L1 CPS<1, and KEYNOTE-355 1≤CPS<10 subgroups. In the KEYNOTE-119 CPS<1 subgroup, the risk of tumor progression was increased with pembrolizumab (HR, 2.23; 95% CI, 1.62 to 3.08; p<0.001), as well as in the 1≤CPS<10 subgroup (HR, 1.64; 95% CI, 1.22 to 2.20; p<0.001). A pooled analysis using a scoring system found no significant difference in OS and PFS among the subgroups with an IC of <1% between immunochemotherapy and chemotherapy. OS (HR, 1.07; 95% CI, 0.91 to 1.26), PFS (HR, 0.96; 95% CI, 0.84 to 1.10), and DOR were also not significantly different in pooled analysis of first-line trials for those with low PD-L1 expression. CONCLUSION ICI-based regimens are not associated with a survival benefit versus chemotherapy in subgroups of advanced/metastatic TNBC that express low PD-L1 levels.
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Affiliation(s)
- Yan Li
- Department of Clinical Pharmacy, Guangxi Academy of Medical Sciences and the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xueyan Liang
- Phase 1 Clinical Trial Laboratory, Guangxi Academy of Medical Sciences and the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Huijuan Li
- Phase 1 Clinical Trial Laboratory, Guangxi Academy of Medical Sciences and the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xiaoyu Chen
- Department of Clinical Pharmacy, Guangxi Academy of Medical Sciences and the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
- Phase 1 Clinical Trial Laboratory, Guangxi Academy of Medical Sciences and the People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China
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22
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Zhang T, Liu J, Wang M, Liu X, Qu J, Zhang H. Prognosis stratification and response to treatment in breast cancer based on one-carbon metabolism-related signature. Front Oncol 2024; 13:1288909. [PMID: 38239641 PMCID: PMC10794736 DOI: 10.3389/fonc.2023.1288909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction Breast cancer (BC) is the most common malignant tumor in the female population. Despite staging and treatment consensus guidelines, significant heterogeneity exists in BC patients' prognosis and treatment efficacy. Alterations in one-carbon (1C) metabolism are critical for tumor growth, but the value of the role of 1C metabolism in BC has not been fully investigated. Methods To investigate the prognostic value of 1C metabolism-related genes in BC, 72 1C metabolism-related genes from GSE20685 dataset were used to construct a risk-score model via univariate Cox regression analysis and the least absolute shrinkage and selection operator (LASSO) regression algorithm, which was validated on three external datasets. Based on the risk score, all BC patients were categorized into high-risk and low-risk groups. The predictive ability of the model in the four datasets was verified by plotting Kaplan-Meier curve and receiver operating characteristic (ROC) curve. The candidate genes were then analyzed in relation to gene mutations, gene enrichment pathways, immune infiltration, immunotherapy, and drug sensitivity. Results We identified a 7-gene 1C metabolism-related signature for prognosis and structured a prognostic model. ROC analysis demonstrated that the model accurately predicted the 2-, 3-, and 5-year overall survival rate of BC patients in the four cohorts. Kaplan-Meier analysis revealed that survival time of high-risk patients was markedly shorter than that of low-risk patients (p < 0.05). Meanwhile, high-risk patients had a higher tumor mutational burden (TMB), enrichment of tumor-associated pathways such as the IL-17 signaling pathway, lower levels of T follicular helper (Tfh) and B cells naive infiltration, and poorer response to immunotherapy. Furthermore, a strong correlation was found between MAT2B and CHKB and immune checkpoints. Discussion These findings offer new insights into the effect of 1C metabolism in the onset, progression, and therapy of BC and can be used to assess BC patients' prognosis, study immune infiltration, and develop potentially more effective clinical treatment options.
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Affiliation(s)
| | | | | | | | - Jia Qu
- Department of Ultrasound, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Huawei Zhang
- Department of Ultrasound, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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SHEN JUAN, ZHANG WEIYU, JIN QINQIN, GONG FUYU, ZHANG HEPING, XU HONGLIANG, LI JIEJIE, YAO HUI, JIANG XIYA, YANG YINTING, HONG LIN, MEI JIE, SONG YANG, ZHOU SHUGUANG. Polo-like kinase 1 as a biomarker predicts the prognosis and immunotherapy of breast invasive carcinoma patients. Oncol Res 2023; 32:339-351. [PMID: 38186570 PMCID: PMC10765123 DOI: 10.32604/or.2023.030887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 08/03/2023] [Indexed: 01/09/2024] Open
Abstract
Background Invasive breast carcinoma (BRCA) is associated with poor prognosis and high risk of mortality. Therefore, it is critical to identify novel biomarkers for the prognostic assessment of BRCA. Methods The expression data of polo-like kinase 1 (PLK1) in BRCA and the corresponding clinical information were extracted from TCGA and GEO databases. PLK1 expression was validated in diverse breast cancer cell lines by quantitative real-time polymerase chain reaction (qRT-PCR) and western blotting. Single sample gene set enrichment analysis (ssGSEA) was performed to evaluate immune infiltration in the BRCA microenvironment, and the random forest (RF) and support vector machine (SVM) algorithms were used to screen for the hub infiltrating cells and calculate the immunophenoscore (IPS). The RF algorithm and COX regression model were applied to calculate survival risk scores based on the PLK1 expression and immune cell infiltration. Finally, a prognostic nomogram was constructed with the risk score and pathological stage, and its clinical potential was evaluated by plotting calibration charts and DCA curves. The application of the nomogram was further validated in an immunotherapy cohort. Results PLK1 expression was significantly higher in the tumor samples in TCGA-BRCA cohort. Furthermore, PLK1 expression level, age and stage were identified as independent prognostic factors of BRCA. While the IPS was unaffected by PLK1 expression, the TMB and MATH scores were higher in the PLK1-high group, and the TIDE scores were higher for the PLK1-low patients. We also identified 6 immune cell types with high infiltration, along with 11 immune cell types with low infiltration in the PLK1-high tumors. A risk score was devised using PLK1 expression and hub immune cells, which predicted the prognosis of BRCA patients. In addition, a nomogram was constructed based on the risk score and pathological staging, and showed good predictive performance. Conclusions PLK1 expression and immune cell infiltration can predict post-immunotherapy prognosis of BRCA patients.
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Affiliation(s)
- JUAN SHEN
- School of Big Data and Artificial Intelligence, Anhui Xinhua University, Hefei, 230088, China
| | - WEIYU ZHANG
- Department of Gynecology and Obstetrics, Maternity and Child Healthcare Hospital Affiliated to Anhui Medical University, Anhui Province Maternity and Child Healthcare Hospital, Hefei, 230001, China
- Department of Gynecology and Obstetrics, The Fifth Clinical College of Anhui Medical University, Hefei, 230032, China
| | - QINQIN JIN
- Department of Gynecology and Obstetrics, Maternity and Child Healthcare Hospital Affiliated to Anhui Medical University, Anhui Province Maternity and Child Healthcare Hospital, Hefei, 230001, China
- Department of Gynecology and Obstetrics, The Fifth Clinical College of Anhui Medical University, Hefei, 230032, China
| | - FUYU GONG
- Departments of Breast Surgery, Fuyang Women and Children’s Hospital, Fuyang, 236000, China
| | - HEPING ZHANG
- Departments of Pathology, Anhui Province Maternity and Child Health Hospital, Hefei, 230001, China
| | - HONGLIANG XU
- Departments of Pathology, Anhui Province Maternity and Child Health Hospital, Hefei, 230001, China
| | - JIEJIE LI
- Department of Gynecology and Obstetrics, Maternity and Child Healthcare Hospital Affiliated to Anhui Medical University, Anhui Province Maternity and Child Healthcare Hospital, Hefei, 230001, China
- Department of Gynecology and Obstetrics, The Fifth Clinical College of Anhui Medical University, Hefei, 230032, China
| | - HUI YAO
- Department of Gynecology and Obstetrics, Maternity and Child Healthcare Hospital Affiliated to Anhui Medical University, Anhui Province Maternity and Child Healthcare Hospital, Hefei, 230001, China
- Department of Gynecology and Obstetrics, The Fifth Clinical College of Anhui Medical University, Hefei, 230032, China
| | - XIYA JIANG
- Department of Gynecology and Obstetrics, Maternity and Child Healthcare Hospital Affiliated to Anhui Medical University, Anhui Province Maternity and Child Healthcare Hospital, Hefei, 230001, China
- Department of Gynecology and Obstetrics, The Fifth Clinical College of Anhui Medical University, Hefei, 230032, China
| | - YINTING YANG
- Department of Gynecology and Obstetrics, Maternity and Child Healthcare Hospital Affiliated to Anhui Medical University, Anhui Province Maternity and Child Healthcare Hospital, Hefei, 230001, China
- Department of Gynecology and Obstetrics, The Fifth Clinical College of Anhui Medical University, Hefei, 230032, China
| | - LIN HONG
- Department of Gynecology and Obstetrics, Maternity and Child Healthcare Hospital Affiliated to Anhui Medical University, Anhui Province Maternity and Child Healthcare Hospital, Hefei, 230001, China
- Department of Gynecology and Obstetrics, The Fifth Clinical College of Anhui Medical University, Hefei, 230032, China
| | - JIE MEI
- Department of Gynecology and Obstetrics, Maternity and Child Healthcare Hospital Affiliated to Anhui Medical University, Anhui Province Maternity and Child Healthcare Hospital, Hefei, 230001, China
- Department of Gynecology and Obstetrics, The Fifth Clinical College of Anhui Medical University, Hefei, 230032, China
| | - YANG SONG
- Department of Pain, The First Affiliated Hospital of Anhui Medical University, Hefei, 230032, China
| | - SHUGUANG ZHOU
- Department of Gynecology and Obstetrics, Maternity and Child Healthcare Hospital Affiliated to Anhui Medical University, Anhui Province Maternity and Child Healthcare Hospital, Hefei, 230001, China
- Department of Gynecology and Obstetrics, The Fifth Clinical College of Anhui Medical University, Hefei, 230032, China
- Department of Gynecology and Obstetrics, Linquan Maternity and Child Healthcare Hospital, Fuyang, 236400, China
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Shi A, Yan M, Pang B, Pang L, Wang Y, Lan Y, Zhang X, Xu J, Ping Y, Hu J. Dissecting cellular states of infiltrating microenvironment cells in melanoma by integrating single-cell and bulk transcriptome analysis. BMC Immunol 2023; 24:52. [PMID: 38082384 PMCID: PMC10714533 DOI: 10.1186/s12865-023-00587-8] [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: 05/25/2022] [Accepted: 11/13/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Cellular states of different immune cells can affect the activity of the whole immune microenvironment. METHODS Here, leveraging reference profiles of microenvironment cell states that were constructed based on single-cell RNA-seq data of melanoma, we dissected the composition of microenvironment cell states across 463 skin cutaneous melanoma (SKCM) bulk samples through CIBERSORT-based deconvolution of gene expression profiles and revealed high heterogeneity of their distribution. Correspondence analysis on the estimated cellular fractions of melanoma bulk samples was performed to identify immune phenotypes. Based on the publicly available clinical survival and therapy data, we analyzed the relationship between immune phenotypes and clinical outcomes of melanoma. RESULTS By analysis of the relationships among those cell states, we further identified three distinct tumor microenvironment immune phenotypes: "immune hot/active", "immune cold-suppressive" and "immune cold-exhausted". They were characterized by markedly different patterns of cell states: most notably the CD8 T Cytotoxic state, CD8 T Mixed state, B non-regulatory state and cancer-associated fibroblasts (CAFs), depicting distinct types of antitumor immune response (or immune activity). These phenotypes had prognostic significance for progression-free survival and implications in response to immune therapy in an independent cohort of anti-PD1 treated melanoma patients. CONCLUSIONS The proposed strategy of leveraging single-cell data to dissect the composition of microenvironment cell states in individual bulk tumors can also extend to other cancer types, and our results highlight the importance of microenvironment cell states for the understanding of tumor immunity.
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Affiliation(s)
- Aiai Shi
- School of Intelligent Medicine and Biotechnology, Guilin Medical University, Guilin, 541100, Guangxi, China
| | - Min Yan
- Department of Immunology, College of Basic Medicine, Chongqing Medical University, Chongqing, 400010, China
| | - Bo Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Lin Pang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yihan Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Yujia Lan
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Xinxin Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China
| | - Jinyuan Xu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Yanyan Ping
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
| | - Jing Hu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, Heilongjiang, China.
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Guo Z, Han S. Targeting cancer stem cell plasticity in triple-negative breast cancer. EXPLORATION OF TARGETED ANTI-TUMOR THERAPY 2023; 4:1165-1181. [PMID: 38213533 PMCID: PMC10776602 DOI: 10.37349/etat.2023.00190] [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: 06/05/2023] [Accepted: 10/15/2023] [Indexed: 01/13/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is a highly aggressive breast cancer subtype with limited treatment options. Cancer stem cells (CSCs) are thought to play a crucial role in TNBC progression and resistance to therapy. CSCs are a small subpopulation of cells within tumors that possess self-renewal and differentiation capabilities and are responsible for tumor initiation, maintenance, and metastasis. CSCs exhibit plasticity, allowing them to switch between states and adapt to changing microenvironments. Targeting CSC plasticity has emerged as a promising strategy for TNBC treatment. This review summarizes recent advances in understanding the molecular mechanisms underlying CSC plasticity in TNBC and discusses potential therapeutic approaches targeting CSC plasticity.
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Affiliation(s)
- Zhengwang Guo
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Integration of Chinese and Western Medicine, Peking University Cancer Hospital & Institute, Beijing 100142, China
| | - Shuyan Han
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Integration of Chinese and Western Medicine, Peking University Cancer Hospital & Institute, Beijing 100142, China
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Tian Q, Liu X, Li A, Wu H, Xie Y, Zhang H, Wu F, Chen Y, Bai C, Zhang X. LINC01936 inhibits the proliferation and metastasis of lung squamous cell carcinoma probably by EMT signaling and immune infiltration. PeerJ 2023; 11:e16447. [PMID: 38084139 PMCID: PMC10710776 DOI: 10.7717/peerj.16447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 10/21/2023] [Indexed: 12/18/2023] Open
Abstract
Purpose To discover the biological function and potential mechanism of LINC01936 in the development of lung squamous cell carcinoma (LUSC). Methods Transcriptome data of LUSC from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases were used to analyze the differentially expressed lncRNAs in LUSC and normal tissues by R "DEseq2", "edgeR" and "limma" packages. The subcellular localization of LINC01936 was predicted by lncLocator. Cell proliferation and apoptosis were measured by CCK-8, MTT assay and Hoechst fluorescence staining. The migration and invasion were detected by Transwell assay. The function and pathway enrichment analysis were performed by Gene Ontology (GO) terms, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and gene set variation analysis (GSVA). The downstream targets of LINC01936 were predicted using RNA-Protein Interaction Prediction (RPISeq) program. The effect of LINC01936 on tumor immune infiltration was analyzed using Pearson Correlation Analysis using R "ggpubr" package. Results Based on the gene expression data of LUSC from TCGA database, 1,603, 1,702 and 529 upregulated and 536, 436 and 630 downregulated lncRNAs were obtained by DEseq2, edgeR and limma programs, respectively. For GSE88862 dataset, we acquired 341 differentially expressed lncRNAs (206 upregulated and 135 downregulated). Venn plot for the intersection of above differential expressed lncRNAs showed that there were 29 upregulated and 23 downregulated genes. LINC01936 was one of downregulated lncRNAs in LUSC tissues. The biological analysis showed that the overexpression of LINC01936 significantly reduced proliferation, migration and invasion of LUSC cells, and promoted cell apoptosis. The knockdown of LINC01936 promoted cell proliferation and metastasis. Pathway and GSVA analysis indicated that LINC01936 might participated in DNA repair, complement, cell adhesion and EMT, etc. LINC01936 was predicted to interact with TCF21, AOC3, RASL12, MEOX2 or HSPB7, which are involved in EMT and PI3K-AKT-MTOR pathway, etc. The expression of LINC01936 was also positively correlated with the infiltrating immune cells in LUSC. Conclusions LINC01936 is downregulated in LUSC. LINC01936 affected proliferation, migration and invasion of LUSC cells probably by EMT and immune infiltration, which might serve as a new target for the treatment of LUSC.
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Affiliation(s)
- Qinqin Tian
- The Second Affiliated Hospital of Army Medical University, Department of Clinical Laboratory, Chongqing, China
- North China University of Science and Technology, College of Life Science, Tangshan, China
| | - Xiyao Liu
- North China University of Science and Technology, College of Life Science, Tangshan, China
| | - Ang Li
- North China University of Science and Technology, School of Public Health, Tangshan, China
| | - Hongjiao Wu
- North China University of Science and Technology, School of Public Health, Tangshan, China
| | - Yuning Xie
- North China University of Science and Technology, School of Public Health, Tangshan, China
| | - Hongmei Zhang
- North China University of Science and Technology, School of Public Health, Tangshan, China
| | - Fengjun Wu
- North China University of Science and Technology, College of Life Science, Tangshan, China
| | - Yating Chen
- North China University of Science and Technology, College of Life Science, Tangshan, China
| | - Congcong Bai
- North China University of Science and Technology, College of Life Science, Tangshan, China
| | - Xuemei Zhang
- North China University of Science and Technology, College of Life Science, Tangshan, China
- North China University of Science and Technology, School of Public Health, Tangshan, China
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Hart S, Garcia V, Dudgeon SN, Hanna MG, Li X, Blenman KRM, Elfer K, Ly A, Salgado R, Saltz J, Gupta R, Hytopoulos E, Larsimont D, Lennerz J, Gallas BD. Initial interactions with the FDA on developing a validation dataset as a medical device development tool. J Pathol 2023; 261:378-384. [PMID: 37794720 PMCID: PMC10841854 DOI: 10.1002/path.6208] [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: 07/14/2023] [Accepted: 08/24/2023] [Indexed: 10/06/2023]
Abstract
Quantifying tumor-infiltrating lymphocytes (TILs) in breast cancer tumors is a challenging task for pathologists. With the advent of whole slide imaging that digitizes glass slides, it is possible to apply computational models to quantify TILs for pathologists. Development of computational models requires significant time, expertise, consensus, and investment. To reduce this burden, we are preparing a dataset for developers to validate their models and a proposal to the Medical Device Development Tool (MDDT) program in the Center for Devices and Radiological Health of the U.S. Food and Drug Administration (FDA). If the FDA qualifies the dataset for its submitted context of use, model developers can use it in a regulatory submission within the qualified context of use without additional documentation. Our dataset aims at reducing the regulatory burden placed on developers of models that estimate the density of TILs and will allow head-to-head comparison of multiple computational models on the same data. In this paper, we discuss the MDDT preparation and submission process, including the feedback we received from our initial interactions with the FDA and propose how a qualified MDDT validation dataset could be a mechanism for open, fair, and consistent measures of computational model performance. Our experiences will help the community understand what the FDA considers relevant and appropriate (from the perspective of the submitter), at the early stages of the MDDT submission process, for validating stromal TIL density estimation models and other potential computational models. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland. This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- Steven Hart
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester MN, USA
| | - Victor Garcia
- Division of Imaging, Diagnostics, and Software Reliability, Office Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, USA
| | - Sarah N. Dudgeon
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | | | - Xiaoxian Li
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA, USA
| | - Kim RM Blenman
- Department of Internal Medicine, Section of Medical Oncology, School of Medicine, Yale University, New Haven, CT, USA
- Department of Computer Science, School of Engineering and Applied Science, Yale University, New Haven, CT, USA
| | - Katherine Elfer
- Division of Imaging, Diagnostics, and Software Reliability, Office Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, USA
| | - Amy Ly
- Department of Pathology, Massachusetts General Hospital, MA, USA
| | - Roberto Salgado
- Department of Pathology, GZA-ZNA Hospitals, Antwerp, Belgium
- Division of Research, Peter Mac Callum Cancer Centre, Melbourne, Australia
| | - Joel Saltz
- Department of Biomedical Informatics, Stony Brook School of Medicine, Stony Brook NY, USA
| | - Rajarsi Gupta
- Department of Biomedical Informatics, Stony Brook School of Medicine, Stony Brook NY, USA
| | | | - Denis Larsimont
- Department of Pathology, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Jochen Lennerz
- Massachusetts General Hospital/Massachusetts General Hospital, Center for Integrated Diagnostics, Boston, MA, USA
| | - Brandon D. Gallas
- Division of Imaging, Diagnostics, and Software Reliability, Office Science and Engineering Laboratories, Center for Devices and Radiological Health, US Food and Drug Administration, Silver Spring, MD, USA
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He T, Sun X, Wu C, Yao L, Zhang Y, Liu S, Jiang Y, Li Y, Wang M, Xu Y. PROS1, a clinical prognostic biomarker and tumor suppressor, is associated with immune cell infiltration in breast cancer: A bioinformatics analysis combined with experimental verification. Cell Signal 2023; 112:110918. [PMID: 37827342 DOI: 10.1016/j.cellsig.2023.110918] [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: 06/09/2023] [Revised: 09/12/2023] [Accepted: 10/09/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND PROS1 is an encoding gene that can generate protein S. This protein is a glycoprotein found in plasma that conducts physiological functions with vitamin K. However, the impact of its expression remains absent in the progression and prognosis of breast cancer (BC). METHODS In this study, we comprehensively explored the expression of PROS1 in BC and its relationship with BC patient survival, prognosis, and other clinicopathological features. We investigated how PROS1 influenced the malignant biological behavior of BC cells. A series of enrichment analyses were conducted, and the immune landscape was explored in BC affected by PROS1. We also determined correlations between PROS1 and common drug sensitivities used for BC treatments. RESULTS PROS1 had low expression in BC, which tended to result in poor survival of BC patients. Overexpressed PROS1 inhibited the migration and invasion of BC cells as well as the epithelial-mesenchymal transition process by downregulating SNAIL. Functional enrichment analyses revealed that PROS1 was more active in extracellular matrix (ECM) organization and structural constituent, ECM-receptor interaction, and other pathways with its related genes. PROS1 was also found to affect immune activity, including various immune cells infiltrating BC. BC patients with high PROS1 expression tended to have lower IC50 values of three common medications and obtained better efficacy. CONCLUSIONS PROS1 can become a promising prognostic factor and a possible therapeutic target in BC patients and suppress BC cell metastatic potential. In addition, PROS1 is a crucial factor in immune infiltration in BC.
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Affiliation(s)
- Tianyi He
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang 110001, China
| | - Xiangyu Sun
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang 110001, China
| | - Chen Wu
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang 110001, China
| | - Litong Yao
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang 110001, China
| | - Yingfan Zhang
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang 110001, China
| | - Shiyang Liu
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang 110001, China
| | - Yuhan Jiang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, PKU International Cancer Institute, MOE Key Laboratory of Carcinogenesis and Translational Research and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing 100191, China
| | - Yixiao Li
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, PKU International Cancer Institute, MOE Key Laboratory of Carcinogenesis and Translational Research and State Key Laboratory of Natural and Biomimetic Drugs, Peking University Health Science Center, Beijing 100191, China
| | - Mozhi Wang
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang 110001, China
| | - Yingying Xu
- Department of Breast Surgery, the First Hospital of China Medical University, Shenyang 110001, China.
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29
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Huang C, Deng M, Leng D, Sun B, Zheng P, Zhang XD. MIRS: An AI scoring system for predicting the prognosis and therapy of breast cancer. iScience 2023; 26:108322. [PMID: 38026206 PMCID: PMC10665820 DOI: 10.1016/j.isci.2023.108322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Revised: 09/25/2023] [Accepted: 10/20/2023] [Indexed: 12/01/2023] Open
Abstract
Tumor-infiltrating immune cells (TIICs) and metastasis are crucial characteristics for tumorigenesis. However, the potential role of their combination in breast cancer (BRCA) remains elusive. Herein, on the basis of quantifying TIICs and tumor metastasis together, we established a precise prognostic scoring system named metastatic and immunogenomic risk score (MIRS) using a neural network model. MIRS showed better performance when compared with other published signatures. MIRS stratifies patients into a high risk subtype (MIRShigh) and a low risk subtype (MIRSlow). The MIRShigh patients exhibit significantly lower survival rate compared with MIRSlow patients (P < 0.0001 ), higher response to chemotherapy, but lower response to immunotherapy. Conversely, higher infiltration level of TIICs and significantly prolonged survival (P = 0.029 ) are observed in MIRSlow patients, indicating sensitive response in immunotherapy. This work presents a promising indicator to guide treatment options of the BRCA population and provides a predicted webtool that is almost universally applicable to BRCA patients.
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Affiliation(s)
- Chen Huang
- Dr. Neher’s Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau SAR 999078, China
- State Key laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau SAR 999078, China
| | - Min Deng
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR 999078, China
| | - Dongliang Leng
- CRDA, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR 999078, China
| | - Baoqing Sun
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 511436, China
| | - Peiyan Zheng
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, National Clinical Research Center of Respiratory Disease, Guangzhou Institute of Respiratory Health, First Affiliated Hospital of Guangzhou Medical University, Guangzhou 511436, China
| | - Xiaohua Douglas Zhang
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, KY 40536, USA
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30
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Yamaleyeva DN, Makita N, Hwang D, Haney MJ, Jordan R, Kabanov AV. Poly(2-oxazoline)-Based Polyplexes as a PEG-Free Plasmid DNA Delivery Platform. Macromol Biosci 2023; 23:e2300177. [PMID: 37466165 DOI: 10.1002/mabi.202300177] [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: 04/23/2023] [Revised: 06/25/2023] [Accepted: 07/04/2023] [Indexed: 07/20/2023]
Abstract
The present study expands the versatility of cationic poly(2-oxazoline) (POx) copolymers as a polyethylene glycol (PEG)-free platform for gene delivery to immune cells, such as monocytes and macrophages. Several block copolymers are developed by varying nonionic hydrophilic blocks (poly(2-methyl-2-oxazoline) (pMeOx) or poly(2-ethyl-2-oxazoline) (pEtOx), cationic blocks, and an optional hydrophobic block (poly(2-isopropyl-2-oxazoline) (iPrOx). The cationic blocks are produced by side chain modification of 2-methoxy-carboxyethyl-2-oxazoline (MestOx) block precursor with diethylenetriamine (DET) or tris(2-aminoethyl)amine (TREN). For the attachment of a targeting ligand, mannose, azide-alkyne cycloaddition click chemistry methods are employed. Of the two cationic side chains, polyplexes made with DET-containing copolymers transfect macrophages significantly better than those made with TREN-based copolymer. Likewise, nontargeted pEtOx-based diblock copolymer is more active in cell transfection than pMeOx-based copolymer. The triblock copolymer with hydrophobic block iPrOx performs poorly compared to the diblock copolymer which lacks this additional block. Surprisingly, attachment of a mannose ligand to either copolymer is inhibitory for transfection. Despite similarities in size and design, mannosylated polyplexes result in lower cell internalization compared to nonmannosylated polyplexes. Thus, PEG-free, nontargeted DET-, and pEtOx-based diblock copolymer outperforms other studied structures in the transfection of macrophages and displays transfection levels comparable to GeneJuice, a commercial nonlipid transfection reagent.
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Affiliation(s)
- Dina N Yamaleyeva
- Joint UNC-CH and NC State Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7575, USA
- Center for Nanotechnology in Drug Delivery and Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7575, USA
| | - Naoki Makita
- Center for Nanotechnology in Drug Delivery and Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7575, USA
- Formulation Research & Development Laboratories, Technology Research & Development, Sumitomo Pharma Co., Ltd., Suita, Osaka, 564-0053, Japan
| | - Duhyeong Hwang
- Center for Nanotechnology in Drug Delivery and Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7575, USA
- Department of Pharmaceutical Engineering, Dankook University, 119 Dandae-ro, Dongnam-gu, Cheonan, 31116, South Korea
| | - Matthew J Haney
- Center for Nanotechnology in Drug Delivery and Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7575, USA
| | - Rainer Jordan
- Department Chemie, Technische Universität Dresden, Zellescher Weg 19, 01069, Dresden, Germany
| | - Alexander V Kabanov
- Joint UNC-CH and NC State Department of Biomedical Engineering, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7575, USA
- Center for Nanotechnology in Drug Delivery and Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, 27599-7575, USA
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Tran KA, Addala V, Johnston RL, Lovell D, Bradley A, Koufariotis LT, Wood S, Wu SZ, Roden D, Al-Eryani G, Swarbrick A, Williams ED, Pearson JV, Kondrashova O, Waddell N. Performance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixtures. Nat Commun 2023; 14:5758. [PMID: 37717006 PMCID: PMC10505141 DOI: 10.1038/s41467-023-41385-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/01/2023] [Indexed: 09/18/2023] Open
Abstract
Cells within the tumour microenvironment (TME) can impact tumour development and influence treatment response. Computational approaches have been developed to deconvolve the TME from bulk RNA-seq. Using scRNA-seq profiling from breast tumours we simulate thousands of bulk mixtures, representing tumour purities and cell lineages, to compare the performance of nine TME deconvolution methods (BayesPrism, Scaden, CIBERSORTx, MuSiC, DWLS, hspe, CPM, Bisque, and EPIC). Some methods are more robust in deconvolving mixtures with high tumour purity levels. Most methods tend to mis-predict normal epithelial for cancer epithelial as tumour purity increases, a finding that is validated in two independent datasets. The breast cancer molecular subtype influences this mis-prediction. BayesPrism and DWLS have the lowest combined numbers of false positives and false negatives, and have the best performance when deconvolving granular immune lineages. Our findings highlight the need for more single-cell characterisation of rarer cell types, and suggest that tumour cell compositions should be considered when deconvolving the TME.
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Affiliation(s)
- Khoa A Tran
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
- School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia
| | - Venkateswar Addala
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Rebecca L Johnston
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - David Lovell
- School of Computer Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
- QUT Centre for Data Science, Brisbane, QLD, 4000, Australia
| | - Andrew Bradley
- Faculty of Engineering, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Lambros T Koufariotis
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Scott Wood
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Sunny Z Wu
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Daniel Roden
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Ghamdan Al-Eryani
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Alexander Swarbrick
- Cancer Ecosystems Program, Garvan Institute of Medical Research, Darlinghurst, NSW, 2010, Australia
- School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Elizabeth D Williams
- School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia
- Australian Prostate Cancer Research Centre - Queensland (APCRC-Q) and Queensland Bladder Cancer Initiative (QBCI), Brisbane, QLD, 4000, Australia
| | - John V Pearson
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Olga Kondrashova
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia
| | - Nicola Waddell
- Cancer Program, QIMR Berghofer Medical Research Institute, Brisbane, QLD, 4006, Australia.
- School of Biomedical Sciences, Queensland University of Technology (QUT), Brisbane, QLD, 4000, Australia.
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Zohair B, Chraa D, Rezouki I, Benthami H, Razzouki I, Elkarroumi M, Olive D, Karkouri M, Badou A. The immune checkpoint adenosine 2A receptor is associated with aggressive clinical outcomes and reflects an immunosuppressive tumor microenvironment in human breast cancer. Front Immunol 2023; 14:1201632. [PMID: 37753093 PMCID: PMC10518422 DOI: 10.3389/fimmu.2023.1201632] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/21/2023] [Indexed: 09/28/2023] Open
Abstract
Background The crosstalk between the immune system and cancer cells has aroused considerable interest over the past decades. To escape immune surveillance cancer cells evolve various strategies orchestrating tumor microenvironment. The discovery of the inhibitory immune checkpoints was a major breakthrough due to their crucial contribution to immune evasion. The A2AR receptor represents one of the most essential pathways within the TME. It is involved in several processes such as hypoxia, tumor progression, and chemoresistance. However, its clinical and immunological significance in human breast cancer remains elusive. Methods The mRNA expression and protein analysis were performed by RT-qPCR and immunohistochemistry. The log-rank (Mantel-Cox) test was used to estimate Kaplan-Meier analysis for overall survival. Using large-scale microarray data (METABRIC), digital cytometry was conducted to estimate cell abundance. Analysis was performed using RStudio software (7.8 + 2023.03.0) with EPIC, CIBERSORT, and ImmuneCellAI algorithms. Tumor purity, stromal and immune scores were calculated using the ESTIMATE computational method. Finally, analysis of gene set enrichment (GSEA) and the TISCH2 scRNA-seq database were carried out. Results Gene and protein analysis showed that A2AR was overexpressed in breast tumors and was significantly associated with high grade, elevated Ki-67, aggressive molecular and histological subtypes, as well as poor survival. On tumor infiltrating immune cells, A2AR was found to correlate positively with PD-1 and negatively with CTLA-4. On the other hand, our findings disclosed more profuse infiltration of protumoral cells such as M0 and M2 macrophages, Tregs, endothelial and exhausted CD8+ T cells within A2ARhigh tumors. According to the Single-Cell database, A2AR is expressed in malignant, stromal and immune cells. Moreover, it is related to tumor purity, stromal and immune scores. Our results also revealed that CD8+T cells from A2ARhigh patients exhibited an exhausted functional profile. Finally, GSEA analysis highlighted the association of A2AR with biological mechanisms involved in tumor escape and progression. Conclusion The present study is the first to elucidate the clinical and immunological relevance of A2AR in breast cancer patients. In light of these findings, A2AR could be deemed a promising therapeutic target to overcome immune evasion prevailing within the TME of breast cancer patients.
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Affiliation(s)
- Basma Zohair
- Immuno-Genetics and Human Pathology Laboratory (LIGEP), Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Dounia Chraa
- Team Immunity and Cancer, The Cancer Research Center of Marseille (CRCM), Inserm, 41068, CNRS, UMR7258, Paoli-Calmettes Institute, Aix-Marseille University, UM 105, Marseille, France
| | - Ibtissam Rezouki
- Immuno-Genetics and Human Pathology Laboratory (LIGEP), Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Hamza Benthami
- Immuno-Genetics and Human Pathology Laboratory (LIGEP), Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
| | - Ibtissam Razzouki
- Department of Pathological Anatomy, Ibn Rochd University Hospital Center, Casablanca, Morocco
| | - Mohamed Elkarroumi
- Mohamed VI Oncology Center, Ibn Rochd University Hospital Center, Casablanca, Morocco
| | - Daniel Olive
- Team Immunity and Cancer, The Cancer Research Center of Marseille (CRCM), Inserm, 41068, CNRS, UMR7258, Paoli-Calmettes Institute, Aix-Marseille University, UM 105, Marseille, France
| | - Mehdi Karkouri
- Department of Pathological Anatomy, Ibn Rochd University Hospital Center, Casablanca, Morocco
| | - Abdallah Badou
- Immuno-Genetics and Human Pathology Laboratory (LIGEP), Faculty of Medicine and Pharmacy, Hassan II University, Casablanca, Morocco
- Mohammed VI Center for Research & Innovation, Rabat, Morocco and Mohammed VI University of Sciences and Health, Casablanca, Morocco
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Chen Q, Cai M, Fan X, Liu W, Fang G, Yao S, Xu Y, Li Q, Zhao Y, Zhao K, Liu Z, Chen Z. An artificial intelligence-based ecological index for prognostic evaluation of colorectal cancer. BMC Cancer 2023; 23:763. [PMID: 37592224 PMCID: PMC10433587 DOI: 10.1186/s12885-023-11289-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 08/11/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND AND OBJECTIVE In the tumor microenvironment (TME), the dynamic interaction between tumor cells and immune cells plays a critical role in predicting the prognosis of colorectal cancer. This study introduces a novel approach based on artificial intelligence (AI) and immunohistochemistry (IHC)-stained whole-slide images (WSIs) of colorectal cancer (CRC) patients to quantitatively assess the spatial associations between tumor cells and immune cells. To achieve this, we employ the Morisita-Horn ecological index (Mor-index), which allows for a comprehensive analysis of the spatial distribution patterns between tumor cells and immune cells within the TME. MATERIALS AND METHODS In this study, we employed a combination of deep learning technology and traditional computer segmentation methods to accurately segment the tumor nuclei, immune nuclei, and stroma nuclei within the tumor regions of IHC-stained WSIs. The Mor-index was used to assess the spatial association between tumor cells and immune cells in TME of CRC patients by obtaining the results of cell nuclei segmentation. A discovery cohort (N = 432) and validation cohort (N = 137) were used to evaluate the prognostic value of the Mor-index for overall survival (OS). RESULTS The efficacy of our method was demonstrated through experiments conducted on two datasets comprising a total of 569 patients. Compared to other studies, our method is not only superior to the QuPath tool but also produces better segmentation results with an accuracy of 0.85. Mor-index was quantified automatically by our method. Survival analysis indicated that the higher Mor-index correlated with better OS in the discovery cohorts (HR for high vs. low 0.49, 95% CI 0.27-0.77, P = 0.0014) and validation cohort (0.21, 0.10-0.46, < 0.0001). CONCLUSION This study provided a novel AI-based approach to segmenting various nuclei in the TME. The Mor-index can reflect the immune status of CRC patients and is associated with favorable survival. Thus, Mor-index can potentially make a significant role in aiding clinical prognosis and decision-making.
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Affiliation(s)
- Qicong Chen
- Institute of Computing Science and Technology, Guangzhou University, No. 230, Outer Ring West Road, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, 510080, China
| | - Ming Cai
- Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, 510080, China
- Department of Radiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Xinjuan Fan
- Department of Pathology, Sixth Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Wenbin Liu
- Institute of Computing Science and Technology, Guangzhou University, No. 230, Outer Ring West Road, Guangzhou, 510006, China
| | - Gang Fang
- Institute of Computing Science and Technology, Guangzhou University, No. 230, Outer Ring West Road, Guangzhou, 510006, China
| | - Su Yao
- Department of Pathology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yao Xu
- Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, 510080, China
- Department of Radiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Qian Li
- Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, 510080, China
- Department of Radiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China
| | - Yingnan Zhao
- Institute of Computing Science and Technology, Guangzhou University, No. 230, Outer Ring West Road, Guangzhou, 510006, China
- Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, 510080, China
| | - Ke Zhao
- Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, 510080, China.
- Department of Radiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China.
- Guangdong Provincial People's Hospital, Guangdong Cardiovascular Institute, Guangdong Academy of Medical Sciences, Guangzhou, China.
| | - Zaiyi Liu
- Guangdong Provincial Key Laboratory of Artificial Intelligence in Medical Image Analysis and Application, Guangzhou, 510080, China.
- Department of Radiology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, 510080, China.
| | - Zhihua Chen
- Institute of Computing Science and Technology, Guangzhou University, No. 230, Outer Ring West Road, Guangzhou, 510006, China.
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Zhang W, Qu H, Ma X, Li L, Wei Y, Wang Y, Zeng R, Nie Y, Zhang C, Yin K, Zhou F, Yang Z. Identification of cuproptosis and immune-related gene prognostic signature in lung adenocarcinoma. Front Immunol 2023; 14:1179742. [PMID: 37622116 PMCID: PMC10445162 DOI: 10.3389/fimmu.2023.1179742] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Accepted: 07/12/2023] [Indexed: 08/26/2023] Open
Abstract
Background Cuproptosis is a novel form of programmed cell death that differs from other types such as pyroptosis, ferroptosis, and autophagy. It is a promising new target for cancer therapy. Additionally, immune-related genes play a crucial role in cancer progression and patient prognosis. Therefore, our study aimed to create a survival prediction model for lung adenocarcinoma patients based on cuproptosis and immune-related genes. This model can be utilized to enhance personalized treatment for patients. Methods RNA sequencing (RNA-seq) data of lung adenocarcinoma (LUAD) patients were collected from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. The levels of immune cell infiltration in the GSE68465 cohort were determined using gene set variation analysis (GSVA), and immune-related genes (IRGs) were identified using weighted gene coexpression network analysis (WGCNA). Additionally, cuproptosis-related genes (CRGs) were identified using unsupervised clustering. Univariate COX regression analysis and least absolute shrinkage selection operator (LASSO) regression analysis were performed to develop a risk prognostic model for cuproptosis and immune-related genes (CIRGs), which was subsequently validated. Various algorithms were utilized to explore the relationship between risk scores and immune infiltration levels, and model genes were analyzed based on single-cell sequencing. Finally, the expression of signature genes was confirmed through quantitative real-time PCR (qRT-PCR), immunohistochemistry (IHC), and Western blotting (WB). Results We have identified 5 Oncogenic Driver Genes namely CD79B, PEBP1, PTK2B, STXBP1, and ZNF671, and developed proportional hazards regression models. The results of the study indicate significantly reduced survival rates in both the training and validation sets among the high-risk group. Additionally, the high-risk group displayed lower levels of immune cell infiltration and expression of immune checkpoint compared to the low-risk group.
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Affiliation(s)
- Wentao Zhang
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Haizeng Qu
- Radiotherapy Department, Dongming People’s Hospital, Heze, Shandong, China
| | - Xiaoqing Ma
- Radiotherapy and Minimally Invasive Group I, The Second Affiliated Hospital of Shandong First Medical University, Taian, Shandong, China
| | - Liang Li
- Department of Thoracic Surgery, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Shandong, China
| | - Yanjun Wei
- Department of Radiation Oncology, Weifang People's Hospital, Weifang, China
| | - Ye Wang
- Tumor Research and Therapy Center, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Renya Zeng
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Yuanliu Nie
- Tumor Research and Therapy Center, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Chenggui Zhang
- Department of Orthopedics, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Ke Yin
- Department of Pathology, Shandong Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, Shandong, China
| | - Fengge Zhou
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
| | - Zhe Yang
- Tumor Research and Therapy Center, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong, China
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Zhang G, Yin Z, Fang J, Wu A, Chen G, Cao K. Construction of the novel immune risk scoring system related to CD8 + T cells in uterine corpus endometrial carcinoma. Cancer Cell Int 2023; 23:124. [PMID: 37349706 DOI: 10.1186/s12935-023-02966-y] [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: 02/14/2023] [Accepted: 06/07/2023] [Indexed: 06/24/2023] Open
Abstract
BACKGROUND Uterine corpus endometrial carcinoma (UCEC) is a gynecological malignant tumor with high incidence and poor prognosis. Although immunotherapy has brought significant survival benefits to advanced UCEC patients, traditional evaluation indicators cannot accurately identify all potential beneficiaries of immunotherapy. Consequently, it is necessary to construct a new scoring system to predict patient prognosis and responsiveness of immunotherapy. METHODS CIBERSORT combined with weighted gene co-expression network analysis (WGCNA), non-negative matrix factorization (NMF), and random forest algorithms to screen the module associated with CD8+ T cells, and key genes related to prognosis were selected out by univariate, least absolute shrinkage and selection operator (LASSO) and multivariate Cox regression analyses to develop the novel immune risk score (NIRS). Kaplan-Meier (K-M) analysis was used to compare the difference of survival between high- and low- NIRS groups. We also explored the correlations between NIRS, immune infiltration and immunotherapy, and three external validation sets were used to verify the predictive performance of NIRS. Furthermore, clinical subgroup analysis, mutation analysis, differential expression of immune checkpoints, and drug sensitivity analysis were performed to generate individualized treatments for patients with different risk scores. Finally, gene set variation analysis (GSVA) was conducted to explore the biological functions of NIRS, and qRT-PCR was applied to verify the differential expressions of three trait genes at cellular and tissue levels. RESULTS Among the modules clustered by WGCNA, the magenta module was most positively associated with CD8+ T cells. Three genes (CTSW, CD3D and CD48) were selected to construct NIRS after multiple screening procedures. NIRS was confirmed as an independent prognostic factor of UCEC, and patients with high NIRS had significantly worse prognosis compared to those with low NIRS. The high NIRS group showed lower levels of infiltrated immune cells, gene mutations, and expression of multiple immune checkpoints, indicating reduced sensitivity to immunotherapy. Three module genes were identified as protective factors positively correlated with the level of CD8+ T cells. CONCLUSIONS In this study, we constructed NIRS as a novel predictive signature of UCEC. NIRS not only differentiates patients with distinct prognoses and immune responsiveness, but also guides their therapeutic regimens.
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Affiliation(s)
- Ganghua Zhang
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Zhijing Yin
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Jianing Fang
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Anshan Wu
- Zhuzhou Hospital Affiliated to Xiangya School of Medicine, Central South University, Zhuzhou, China
| | - Guanjun Chen
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China
| | - Ke Cao
- Department of Oncology, Third Xiangya Hospital, Central South University, Changsha, China.
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Ding R, Wang Y, Fan J, Tian Z, Wang S, Qin X, Su W, Wang Y. Identification of immunosuppressive signature subtypes and prognostic risk signatures in triple-negative breast cancer. Front Oncol 2023; 13:1108472. [PMID: 37377907 PMCID: PMC10292819 DOI: 10.3389/fonc.2023.1108472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Accepted: 04/10/2023] [Indexed: 06/29/2023] Open
Abstract
Purpose Immune checkpoint blockade (ICB) therapy has transformed the treatment of triple-negative breast cancer (TNBC) in recent years. However, some TNBC patients with high programmed death-ligand 1 (PD-L1) expression levels develop immune checkpoint resistance. Hence, there is an urgent need to characterize the immunosuppressive tumor microenvironment and identify biomarkers to construct prognostic models of patient survival outcomes in order to understand biological mechanisms operating within the tumor microenvironment. Patients and methods RNA sequence (RNA-seq) data from 303 TNBC samples were analyzed using an unsupervised cluster analysis approach to reveal distinctive cellular gene expression patterns within the TNBC tumor microenvironment (TME). A panel of T cell exhaustion signatures, immunosuppressive cell subtypes and clinical features were correlated with the immunotherapeutic response, as assessed according to gene expression patterns. The test dataset was then used to confirm the occurrence of immune depletion status and prognostic features and to formulate clinical treatment recommendations. Concurrently, a reliable risk prediction model and clinical treatment strategy were proposed based on TME immunosuppressive signature differences between TNBC patients with good versus poor survival status and other clinical prognostic factors. Results Significantly enriched TNBC microenvironment T cell depletion signatures were detected in the analyzed RNA-seq data. A high proportion of certain immunosuppressive cell subtypes, 9 inhibitory checkpoints and enhanced anti-inflammatory cytokine expression profiles were noted in 21.4% of TNBC patients that led to the designation of this group of immunosuppressed patients as the immune depletion class (IDC). Although IDC group TNBC samples contained tumor-infiltrating lymphocytes present at high densities, IDC patient prognosis was poor. Notably, PD-L1 expression was relatively elevated in IDC patients that indicated their cancers were resistant to ICB treatment. Based on these findings, a set of gene expression signatures predicting IDC group PD-L1 resistance was identified then used to develop risk models for use in predicting clinical therapeutic outcomes. Conclusion A novel TNBC immunosuppressive tumor microenvironment subtype associated with strong PD-L1 expression and possible resistance to ICB treatment was identified. This comprehensive gene expression pattern may provide fresh insights into drug resistance mechanisms for use in optimizing immunotherapeutic approaches for TNBC patients.
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Affiliation(s)
- Ran Ding
- Changchun University of Chinese Medicine, Changchun, Jilin, China
- Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Yuhan Wang
- Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Jinyan Fan
- Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Ziyue Tian
- The Affiliated Hospital of Changchun University of Chinese Medicine, Jilin, China
| | - Shuang Wang
- Department of Traditional Chinese Medicine, The First Hospital of Jilin University, Changchun, Jilin, China
| | - Xiujuan Qin
- Anhui University of Chinese Medicine, Hefei, Anhui, China
| | - Wei Su
- Changchun University of Chinese Medicine, Changchun, Jilin, China
| | - Yanbo Wang
- Changchun University of Chinese Medicine, Changchun, Jilin, China
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Fonseca-Montaño MA, Vázquez-Santillán KI, Hidalgo-Miranda A. The current advances of lncRNAs in breast cancer immunobiology research. Front Immunol 2023; 14:1194300. [PMID: 37342324 PMCID: PMC10277570 DOI: 10.3389/fimmu.2023.1194300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Breast cancer is the most frequently diagnosed malignancy and the leading cause of cancer-related death in women worldwide. Breast cancer development and progression are mainly associated with tumor-intrinsic alterations in diverse genes and signaling pathways and with tumor-extrinsic dysregulations linked to the tumor immune microenvironment. Significantly, abnormal expression of lncRNAs affects the tumor immune microenvironment characteristics and modulates the behavior of different cancer types, including breast cancer. In this review, we provide the current advances about the role of lncRNAs as tumor-intrinsic and tumor-extrinsic modulators of the antitumoral immune response and the immune microenvironment in breast cancer, as well as lncRNAs which are potential biomarkers of tumor immune microenvironment and clinicopathological characteristics in patients, suggesting that lncRNAs are potential targets for immunotherapy in breast cancer.
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Affiliation(s)
- Marco Antonio Fonseca-Montaño
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | | | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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Aristei C, Kaidar-Person O, Boersma L, Leonardi MC, Offersen B, Franco P, Arenas M, Bourgier C, Pfeffer R, Kouloulias V, Bölükbaşı Y, Meattini I, Coles C, Luis AM, Masiello V, Palumbo I, Morganti AG, Perrucci E, Tombolini V, Krengli M, Marazzi F, Trigo L, Borghesi S, Ciabattoni A, Ratoša I, Valentini V, Poortmans P. The 2022 Assisi Think Tank Meeting: White paper on optimising radiation therapy for breast cancer. Crit Rev Oncol Hematol 2023:104035. [PMID: 37244324 DOI: 10.1016/j.critrevonc.2023.104035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/11/2023] [Accepted: 05/23/2023] [Indexed: 05/29/2023] Open
Abstract
The present white paper, referring to the 4th Assisi Think Tank Meeting on breast cancer, reviews state-of-the-art data, on-going studies and research proposals. < 70% agreement in an online questionnaire identified the following clinical challenges: 1: Nodal RT in patients who have a) 1-2 positive sentinel nodes without ALND (axillary lymph node dissection); b) cN1 disease transformed into ypN0 by primary systemic therapy and c) 1-3 positive nodes after mastectomy and ALND. 2. The optimal combination of RT and immunotherapy (IT), patient selection, IT-RT timing, and RT optimal dose, fractionation and target volume. Most experts agreed that RT- IT combination does not enhance toxicity. 3: Re-irradiation for local relapse converged on the use of partial breast irradiation after second breast conserving surgery. Hyperthermia aroused support but is not widely available. Further studies are required to finetune best practice, especially given the increasing use of re-irradiation.
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Affiliation(s)
- C Aristei
- Radiation Oncology Section, Department of Medicine and Surgery, University of Perugia and Perugia General Hospital, Perugia, Italy.
| | - O Kaidar-Person
- Breast Radiation Unit, Radiation Oncology, Sheba Medical Center, Ramat Gan, Israel
| | - L Boersma
- Radiation Oncology (Maastro), GROW School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, the Netherlands
| | - M C Leonardi
- Division of Radiation Oncology, IEO European Institute of Oncology, IRCCS, Milan, Italy
| | - B Offersen
- Department of Experimental Clinical Oncology, Department of Oncology, Danish Centre for Particle Therapy, Aarhus University Hospital, Aarhus, Denmark
| | - P Franco
- Depatment of Translational Medicine, University of Eastern Piedmont and Department of Radiation Oncology, 'Maggiore della Carita`' University Hospital, Novara, Italy
| | - M Arenas
- Universitat Rovira I Virgili, Radiation Oncology Department, Hospital Universitari Sant Hoan de Reus, IISPV, Spain
| | - C Bourgier
- Radiation Oncology, ICM-Val d' Aurelle, Univ Montpellier, Montpellier, France
| | - R Pfeffer
- Oncology Institute, Assuta Medical Center, Tel Aviv and Ben Gurion University Medical School, Israel
| | - V Kouloulias
- 2nd Department of Radiology, Radiotherapy Unit, Medical School, National and Kapodistrian University of Athens, Greece
| | - Y Bölükbaşı
- Koc University, Faculty of Medicine, Department of Radiation Oncology, Istanbul, Turkey
| | - I Meattini
- Department of Experimental and Clinical Biomedical Sciences "M. Serio", University of Florence & Radiation Oncology Unit - Oncology Department, Azienda Ospedaliero Universitaria Careggi, Florence, Italy
| | - C Coles
- Department of Oncology, University of Cambridge, UK
| | - A Montero Luis
- Department of Radiation Oncology, University Hospital HM Sanchinarro, HM Hospitales, Madrid, Spain
| | - V Masiello
- Unità Operativa di Radioterapia Oncologica, Dipartimento di Diagnostica per Immagine, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Gemelli IRCSS Roma, Italy
| | - I Palumbo
- Radiation Oncology Section, Department of Medicine and Surgery, University of Perugia and Perugia General Hospital, Perugia, Italy
| | - A G Morganti
- DIMES, Alma Mater Studiorum Bologna University, Bologna, Italy; Radiation Oncology, IRCCS Azienda Ospedaliero-Universitaria di Bologna, Alma Mater Studiorum Bologna University; Bologna, Italy
| | - E Perrucci
- Radiation Oncology Section, Perugia General Hospital, Perugia, Italy
| | - V Tombolini
- Radiation Oncology, Department of Radiological, Oncological and Pathological Science, University "La Sapienza", Roma, Italy
| | - M Krengli
- DISCOG, Università di Padova e Istituto Oncologico Veneto - IRCCS
| | - F Marazzi
- Unità Operativa di Radioterapia Oncologica, Dipartimento di Diagnostica per Immagine, Radioterapia Oncologica ed Ematologia, Fondazione Policlinico Gemelli IRCSS Roma, Italy
| | - L Trigo
- Service of Brachytherapy, Department of Image and Radioncology, Instituto Português Oncologia Porto Francisco Gentil E.P.E., Portugal
| | - S Borghesi
- Radiation Oncology Unit of Arezzo-Valdarno, Azienda USL Toscana Sud Est, Italy
| | - A Ciabattoni
- Department of Radiation Oncology, San Filippo Neri Hospital, ASL Rome 1, Rome, Italy
| | - I Ratoša
- Division of Radiation Oncology, Institute of Oncology Ljubljana, Ljubljana, Slovenia; Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - V Valentini
- Dipartimento di Diagnostica per Immagini, Radioterapia Oncologica ed Ematologia, Università Cattolica del Sacro Cuore e Fondazione Policlinico Gemelli IRCSS Roma, Italy
| | - P Poortmans
- Department of Radiation Oncology, Iridium Kankernetwerk, Antwerp, Belgium; University of Antwerp, Faculty of Medicine and Health Sciences, Antwerp, Belgium
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Xu J, Yang Z, Xie W, Wan R, Li C, Fei K, Sun B, Yang X, Chen P, Meng F, Wang G, Zhao J, Han Y, Cai S, Wang J, Wang Z. A prognostic and immunotherapeutic predictive model based on the cell-originated characterization of tumor microenvironment in lung adenocarcinoma. iScience 2023; 26:106616. [PMID: 37168563 PMCID: PMC10165414 DOI: 10.1016/j.isci.2023.106616] [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: 01/06/2023] [Revised: 02/24/2023] [Accepted: 04/04/2023] [Indexed: 05/13/2023] Open
Abstract
Tumor microenvironment (TME) plays a crucial role in predicting prognosis and response to therapy in lung cancer. Our study established a prognostic and immunotherapeutic predictive model, the tumor immune cell score (TICS), by differentiating cell origins in lung adenocarcinoma (LUAD) based on the transcriptomic data of 2,510 patients in 14 independent cohorts, including 12 public datasets and two in-house cohorts. The high TICS was associated with prolonged overall survival (OS), especially in the early-stage LUAD. For the advanced-stage LUAD, high TICS predicted a superior OS in patients who were treated with immunotherapy instead of chemotherapy or TKI. The result suggested that TICS could serve as an indicator for the prognostic stratification management of patients in the early-stage LUAD, and as a potential guide for therapeutic decision-marking in the advanced-stage LUAD. Our findings provided an insight into prognosis stratification and potential guidance for treatment strategy selection.
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Affiliation(s)
- Jiachen Xu
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
- Guangdong Provincial People’s Hospital/Guangdong Provincial Academy of Medical Sciences, Guangdong Provincial Key Lab of Translational Medicine in Lung Cancer, Guangdong 510317, P.R. China
| | - Zhenlin Yang
- Department of Thoracic Surgery, National Cancer Center/ National Clinical Research Center for Cancer/ Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | - Wenchuan Xie
- Burning Rock Biotech, Guangdong 510300, P.R. China
| | - Rui Wan
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | | | - Kailun Fei
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | - Boyang Sun
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | - Xu Yang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | - Ping Chen
- Department of Oncology, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School, The First People’s Hospital of Yancheng; Jiangsu 224001, P.R. China
| | - Fanqi Meng
- Burning Rock Biotech, Guangdong 510300, P.R. China
| | | | - Jing Zhao
- Burning Rock Biotech, Guangdong 510300, P.R. China
| | - Yusheng Han
- Burning Rock Biotech, Guangdong 510300, P.R. China
| | - Shangli Cai
- Burning Rock Biotech, Guangdong 510300, P.R. China
| | - Jie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
| | - Zhijie Wang
- State Key Laboratory of Molecular Oncology, Department of Medical Oncology, National Cancer Center/ National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100021, P.R. China
- Corresponding author
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Fonseca-Montaño MA, Cisneros-Villanueva M, Coales I, Hidalgo-Miranda A. LINC00426 is a potential immune phenotype-related biomarker and an overall survival predictor in PAM50 luminal B breast cancer. Front Genet 2023; 14:1034569. [PMID: 37260772 PMCID: PMC10228735 DOI: 10.3389/fgene.2023.1034569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/03/2023] [Indexed: 06/02/2023] Open
Abstract
Background: Breast cancer (BRCA) represents the most frequent diagnosed malignancy in women worldwide. Despite treatment advances, BRCAs eventually develop resistance to targeted therapies, resulting in poor prognosis. The identification of new biomarkers, like immune-related long non-coding RNAs (lncRNAs), could contribute to the clinical management of BRCA patients. In this report, we evaluated the LINC00426 expression in PAM50 BRCA subtypes from two clinical independent cohorts (BRCA-TCGA and GEO-GSE96058 datasets). Methods and results: Using Cox regression models and Kaplan-Meier survival analyses, we identified that LINC00426 expression was a consistent overall survival (OS) predictor in luminal B (LB) BRCA patients. Subsequently, differential gene expression and gene set enrichment analyses identified that LINC00426 expression was associated with different immune-related and cancer-related pathways and processes in LB BRCA. Additionally, the LINC00426 expression was correlated with the infiltration level of diverse immune cell populations, alongside immune checkpoint and cytolytic activity-related gene expression. Conclusion: This evidence suggests that LINC00426 is a potential biomarker of immune phenotype and an OS predictor in PAM50 LB BRCA.
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Affiliation(s)
- Marco Antonio Fonseca-Montaño
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
- Programa de Doctorado, Posgrado en Ciencias Biológicas, Unidad de Posgrado, Universidad Nacional Autónoma de México (UNAM), Mexico City, Mexico
| | - Mireya Cisneros-Villanueva
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
| | - Isabelle Coales
- Centre for Host Microbiome Interactions, King’s College London, London, United Kingdom
| | - Alfredo Hidalgo-Miranda
- Laboratorio de Genómica del Cáncer, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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Wu Q, Zheng S, Lin N, Xie X. Comprehensive research into prognostic and immune signatures of transcription factor family in breast cancer. BMC Med Genomics 2023; 16:87. [PMID: 37098532 PMCID: PMC10127334 DOI: 10.1186/s12920-023-01521-y] [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: 11/12/2022] [Accepted: 04/15/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Breast cancer (BRCA) is the most common malignancy with high morbidity and mortality in women, and transcription factor (TF) is closely related to the occurrence and development of BRCA. This study was designed to identify a prognostic gene signature based on TF family to reveal immune characteristics and prognostic survival of BRCA. METHODS In this study, RNA-sequence with corresponding clinical data were obtained from The Cancer Genome Atlas (TCGA) and GSE42568. Prognostic differentially expressed transcription factor family genes (TFDEGs) were screened to construct a risk score model, after which BRCA patients were stratified into low-risk and high-risk groups based on their corresponding risk scores. Kaplan-Meier (KM) analysis was applied to evaluate the prognostic implication of risk score model, and a nomogram model was developed and validated with the TCGA and GSE20685. Furthermore, the GSEA revealed pathological processes and signaling pathways enriched in the low-risk and high-risk groups. Finally, analyses regarding levels of immune infiltration, immune checkpoints and chemotactic factors were all completed to investigate the correlation between the risk score and tumor immune microenvironment (TIME). RESULTS A prognostic 9-gene signature based on TFDEGs was selected to establish a risk score model. According to KM analyses, high-risk group witnessed a significantly worse overall survival (OS) than low-risk group in both TCGA-BRCA and GSE20685. Furthermore, the nomogram model proved great possibility in predicting the OS of BRCA patients. As indicted in GSEA analysis, tumor-associated pathological processes and pathways were relatively enriched in high-risk group, and the risk score was negatively correlated with ESTIMATE score, infiltration levels of CD4+ and CD8+T cells, as well as expression levels of immune checkpoints and chemotactic factors. CONCLUSIONS The prognostic model based on TFDEGs could distinguish as a novel biomarker for predicting prognosis of BRCA patients; in addition, it may also be utilized to identify potential benefit population from immunotherapy in different TIME and predict potential drug targets.
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Affiliation(s)
- Qing Wu
- Department of Oncology, Molecule Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, Fujian, China
- Department of Oncology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China
| | - Shiyao Zheng
- College of Clinical Medicine for Oncology, Fujian Medical University, Fuzhou, Fujian, China
| | - Nan Lin
- Fuzong Clinical Medical College of Fujian Medical University, Fuzhou, Fujian, China
- Department of Gastrointestinal Surgery, The 900th Hospital of Joint Logistics Support Forces of Chinese PLA, Fuzhou, Fujian, China
| | - Xianhe Xie
- Department of Oncology, Molecule Oncology Research Institute, The First Affiliated Hospital of Fujian Medical University, No. 20 Chazhong Road, Fuzhou, 350005, Fujian, China.
- Department of Oncology, National Regional Medical Center, Binhai Campus of the First Affiliated Hospital, Fujian Medical University, Fuzhou, 350212, China.
- Fujian Key Laboratory of Precision Medicine for Cancer, The First Affiliated Hospital of Fujian Medical University, Fuzhou, 350005, China.
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Zhou D, Li M, Yasin MH, Lu Q, Fu J, Jiang K, Hong R, Wang S, Xu F. The prognostic value and immune microenvironment association of AR in HER2+ nonmetastatic breast cancer. NPJ Breast Cancer 2023; 9:30. [PMID: 37085500 PMCID: PMC10121570 DOI: 10.1038/s41523-023-00527-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/30/2023] [Indexed: 04/23/2023] Open
Abstract
This study aimed to investigate the prognostic value of AR in HER2+ nonmetastatic breast invasive ductal carcinoma (IDC) and its relationship with the immune microenvironment. HER2+ nonmetastatic breast IDC patients diagnosed by pathology who underwent surgery at Sun Yat-sen University Cancer Center from 2016 to 2017 were included. AR+ and AR- breast IDC samples were matched 1:1 in age, T stage, and N stage for immune infiltration analysis. A total of 554 patients with HER2+ nonmetastatic breast cancer were included in this retrospective study, regardless of HR status. The cut-off value for AR was set at 10%. ER+ (p < 0.001) and PR+ (p < 0.001) were associated with positive AR expression. Kaplan-Meier survival curve analysis suggested that AR was closely correlated with overall survival (OS) (p = 0.001) but not disease-free survival (DFS) (p = 0.051). After eliminating the potential impact caused by HR, AR also predicted longer OS (p = 0.014) and was an independent predictive factor for OS of HER2+HR- nonmetastatic breast IDC patients, as revealed by multivariate analysis (p = 0.036). For AR+ and AR- matched HER2+HR- patients, TILs (p = 0.043) and PD-L1 (p = 0.027) levels were significantly lower in AR+ patients. The strongest negative correlation was observed between AR and PD-L1 (Pearson's r = -0.299, p = 0.001). AR+ status was markedly related to better OS in HER2+HR- nonmetastatic breast cancer patients, while a negative correlation was observed between AR and PD-L1/TILs. We provide new insights into the prognostic value of AR and its association with the immune microenvironment to optimize treatment strategies in HER2+ nonmetastatic breast IDCs.
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Affiliation(s)
- Danyang Zhou
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
- Department of Oncology, Peking University Shenzhen Hospital, Shenzhen, China
| | - Mei Li
- Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510000, China
| | - Mohamed Hussein Yasin
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Qianyi Lu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Jia Fu
- Department of Pathology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, 510000, China
| | - Kuikui Jiang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Ruoxi Hong
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China
| | - Shusen Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
| | - Fei Xu
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, China.
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Xu SM, Xiao HY, Hu ZX, Zhong XF, Zeng YJ, Wu YX, Li D, Song T. GRN is a prognostic biomarker and correlated with immune infiltration in glioma: A study based on TCGA data. Front Oncol 2023; 13:1162983. [PMID: 37091137 PMCID: PMC10117795 DOI: 10.3389/fonc.2023.1162983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/24/2023] [Indexed: 04/09/2023] Open
Abstract
BackgroundAmong primary brain tumors, gliomas are associated with a poor prognosis and a median survival that varies depending on the tumor grade and subtype. As the most malignant form of glioma, glioblastoma (GBM) constitutes a significant health concern. Alteration in granulin(GRN) has been proved to be accountable for several diseases. However, the relationship between GRN and GBM remains unclear. We evaluated the role of GRN in GBM through The Cancer Genome Atlas (TCGA) databaseMethodsFirst, we assessed the relationship between GRN and GBM through the GEPIA database. Next, the relationship between GRN and GBM prognosis was analyzed by logistic regression and multivariate cox methods. Using CIBERSORT and the GEPIA correlation module, we also investigated the link between GRN and immune infiltrates in cancer. Using the TCGA data, a gene set enrichment analysis (GSEA) was performed. We also employed Tumor Immune Estimation Resource (TIMER) to examine the data set of GRN expression and immune infiltration level in GBM and investigate the cumulative survival in GBM. We also validated tissues from GBM patients by Western blotting, RT-qPCR, and immunohistochemistry.ResultsIncreased GRN expression was shown to have a significant relationship to tumor grade in a univariate study utilizing logistic regression. Furthermore, multivariate analysis disclosed that GRN expression down-regulation is an independent predictive factor for a favorable outcome. GRN expression level positively correlates with the number of CD4+ T cells, neutrophils, macrophages, and dendritic cells (DCs) that infiltrate a GBM. The GSEA also found that the high GRN expression phenotype pathway was enriched for genes involved in immune response molecular mediator production, lymphocyte-mediated immunity, cytokine-mediated signaling pathway, leukocyte proliferation, cell chemotaxis, and CD4+ alpha beta T cell activation. Differentially enriched pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) include lysosome, apoptosis, primary immunodeficiency, chemokine signaling pathway, natural killer cell-mediated cytotoxicity, and B cell receptor signaling pathway. Validated result showed that GRN was upregulated in GBM tissues. These results suggested that GRN was a potential indicator for the status of GBM.ConclusionGRN is a prognostic biomarker and correlated with immune infiltrates in GBM.
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Affiliation(s)
- Su-Mei Xu
- Phase I Clinical Trial Center, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Hai-Yan Xiao
- Phase I Clinical Trial Center, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
| | - Zhong-Xu Hu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xue-Feng Zhong
- Phase I Clinical Trial Center, Xiangya Hospital, Central South University, Changsha, China
| | - You-Jie Zeng
- Department of Anesthesiology, Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - You-Xuan Wu
- Phase I Clinical Trial Center, Xiangya Hospital, Central South University, Changsha, China
| | - Dai Li
- Phase I Clinical Trial Center, Xiangya Hospital, Central South University, Changsha, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Dai Li, ; Tao Song,
| | - Tao Song
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, China
- *Correspondence: Dai Li, ; Tao Song,
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Ren X, Song Y, Pang J, Chen L, Zhou L, Liang Z, Wu H. Prognostic value of various immune cells and Immunoscore in triple-negative breast cancer. Front Immunol 2023; 14:1137561. [PMID: 37090736 PMCID: PMC10117828 DOI: 10.3389/fimmu.2023.1137561] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 03/29/2023] [Indexed: 04/08/2023] Open
Abstract
BackgroundThis study aimed to evaluate the expression status and prognostic role of various immunoregulatory cells and test in triple-negative breast cancer (TNBC).MethodsThe expression of five markers (CD3/CD4/CD8/CD19/CD163) of tumor immune cells was evaluated retrospectively in tumor sections from 68 consecutive cases of TNBC by immunohistochemistry. Computational image analysis was used to quantify the density and distribution of each immune marker within the tumor region, tumor invasive margin, and expression hotspots. Immunoscores were calculated using an automated approach. Other clinical characteristics were also analyzed.ResultsFor all patients, Kaplan–Meier survival analysis showed that high CD3+ signals in the tumor region (disease-free survival (DFS), P=0.0014; overall survival (OS), P=0.0031) and total region (DFS, P=0.0014; OS, P=0.0031) were significantly associated with better survival. High CD4+ levels in the tumor region and total regions were significantly associated with better survival (P<0.05). For Hotspot analysis, CD3+ was associated with significantly better survival for all Top1, Top2, and Top3 densities (DFS and OS, P<0.05). High CD4+ levels were significantly associated with better prognosis for Top1 and Top3 densities (DFS and OS, P<0.05). For stage IIB and IIIC patients, CD3+ in the tumor region and all Top hotspots was found to be significantly correlated with survival (DFS and OS, P<0.05). CD4+ cells were significantly associated with survival in the tumor region, total region, and Top3 density (DFS, P=0.0213; OS, P=0.0728). CD8+ cells were significantly associated with survival in the invasive margin, Top2 density, and Top3 density. Spatial parameter analysis showed that high colocalization of tumor cells and immune cells (CD3+, CD4+, or CD8+) was significantly associated with patient survival.ConclusionComputational image analysis is a reliable tool for evaluating the density and distribution of immune regulatory cells and for calculating the Immunoscore in TNBC. The Immunoscore retains its prognostic significance in TNBC later than IIB stage breast cancer. Future studies are required to confirm its potential to predict tumor responses to chemotherapy and immune therapy.
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Affiliation(s)
- Xinyu Ren
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yu Song
- Department of Breast Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Junyi Pang
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Longyun Chen
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Liangrui Zhou
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhiyong Liang
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Zhiyong Liang, ; Huanwen Wu,
| | - Huanwen Wu
- Department of Pathology, State Key Laboratory of Complex Severe and Rare Disease, Molecular Pathology Research Center, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- *Correspondence: Zhiyong Liang, ; Huanwen Wu,
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Ding R, Liu Q, Yu J, Wang Y, Gao H, Kan H, Yang Y. Identification of Breast Cancer Subtypes by Integrating Genomic Analysis with the Immune Microenvironment. ACS OMEGA 2023; 8:12217-12231. [PMID: 37033796 PMCID: PMC10077467 DOI: 10.1021/acsomega.2c08227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Accepted: 03/14/2023] [Indexed: 06/19/2023]
Abstract
Objectives: We aim to identify the breast cancer (BC) subtype clusters and the crucial gene classifier prognostic signatures by integrating genomic analysis with the tumor immune microenvironment (TME). Methods: Data sets of BC were derived from the Cancer Genome Atlas (TCGA), METABRIC, and Gene Expression Omnibus (GEO) databases. Unsupervised consensus clustering was carried out to obtain the subtype clusters of BC patients. Weighted gene coexpression network analysis (WGCNA), least absolute shrinkage and selection operator (LASSO), and univariate and multivariate regression analysis were employed to obtain the gene classifier signatures and their biological functions, which were validated by the BC dataset from the METABRIC database. Additionally, to evaluate the overall survival rates of BC patients, Kaplan-Meier survival analysis was carried out. Moreover, to assess how BC subtype clusters are related to the TME, single-cell analysis was performed. Finally, the drug sensitivity and the immune cell infiltration for different phenotypes of BC patients were also calculated by the CIBERSORT and ESTIMATE algorithms. Results : TCGA-BC samples were divided into three subtype clusters, S1, S2, and S3, among which the prognosis of S2 was poor and that of S1 and S3 were better. Three key pathways and 10 crucial prognostic-related gene signatures are screened. Finally, single-cell analysis suggests that S1 samples have the most types of immune cells, S2 with more sensitivity to tumor treatment drugs are enriched with more neutrophils, and more multilymphoid progenitor cells are involved in subtype cluster S3. Conclusions: Our novelty was to identify the BC subtype clusters and the gene classifier signatures employing a large-amount dataset combined with multiple bioinformatics methods. All of the results provide a basis for clinical precision treatment of BC.
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Affiliation(s)
- Ran Ding
- School
of Medical Informatics Engineering, Anhui
University of Chinese Medicine, Hefei 230012, China
- Anhui
Computer Application Research Institute of Chinese Medicine, China Academy of Chinese Medical Sciences, Hefei 230013, China
| | - Qiwei Liu
- School
of Medical Informatics Engineering, Anhui
University of Chinese Medicine, Hefei 230012, China
| | - Jing Yu
- School
of Medical Informatics Engineering, Anhui
University of Chinese Medicine, Hefei 230012, China
| | - Yongkang Wang
- School
of Medical Informatics Engineering, Anhui
University of Chinese Medicine, Hefei 230012, China
| | - Honglei Gao
- School
of Medical Informatics Engineering, Anhui
University of Chinese Medicine, Hefei 230012, China
| | - Hongxing Kan
- School
of Medical Informatics Engineering, Anhui
University of Chinese Medicine, Hefei 230012, China
- Anhui
Computer Application Research Institute of Chinese Medicine, China Academy of Chinese Medical Sciences, Hefei 230013, China
| | - Yinfeng Yang
- School
of Medical Informatics Engineering, Anhui
University of Chinese Medicine, Hefei 230012, China
- Anhui
Computer Application Research Institute of Chinese Medicine, China Academy of Chinese Medical Sciences, Hefei 230013, China
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Onkar S, Cui J, Zou J, Cardello C, Cillo AR, Uddin MR, Sagan A, Joy M, Osmanbeyoglu HU, Pogue-Geile KL, McAuliffe PF, Lucas PC, Tseng GC, Lee AV, Bruno TC, Oesterreich S, Vignali DAA. Immune landscape in invasive ductal and lobular breast cancer reveals a divergent macrophage-driven microenvironment. NATURE CANCER 2023; 4:516-534. [PMID: 36927792 PMCID: PMC11194444 DOI: 10.1038/s43018-023-00527-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/10/2023] [Indexed: 03/18/2023]
Abstract
T cell-centric immunotherapies have shown modest clinical benefit thus far for estrogen receptor-positive (ER+) breast cancer. Despite accounting for 70% of all breast cancers, relatively little is known about the immunobiology of ER+ breast cancer in women with invasive ductal carcinoma (IDC) and invasive lobular carcinoma (ILC). To investigate this, we performed phenotypic, transcriptional and functional analyses for a cohort of treatment-naive IDC (n = 94) and ILC (n = 87) tumors. We show that macrophages, and not T cells, are the predominant immune cells infiltrating the tumor bed and the most transcriptionally diverse cell subset between IDC and ILC. Analysis of cellular neighborhoods revealed an interplay between macrophages and T cells associated with longer disease-free survival in IDC but not ILC. Our datasets provide a rich resource for further interrogation into immune cell dynamics in ER+ IDC and ILC and highlight macrophages as a potential target for ER+ breast cancer.
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Affiliation(s)
- Sayali Onkar
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Graduate Program in Microbiology and Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Jian Cui
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Jian Zou
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Carly Cardello
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Anthony R Cillo
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Mostofa Rafid Uddin
- Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA, USA
- Joint Carnegie Mellon University-University of Pittsburgh PhD Program in Computational Biology, Pittsburgh, PA, USA
| | - April Sagan
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Marion Joy
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- NSABP Foundation, Pittsburgh, PA, USA
| | - Hatice U Osmanbeyoglu
- Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Priscilla F McAuliffe
- Section of Breast Surgery, Division of Surgical Oncology, Department of Surgery, University of Pittsburgh College of Medicine, Magee Women's Hospital of UPMC, Pittsburgh, PA, USA
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Peter C Lucas
- UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- NSABP Foundation, Pittsburgh, PA, USA
- Department of Pathology, University of Pittsburgh, Pittsburgh, PA, USA
- Cancer Biology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - George C Tseng
- Department of Biostatistics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Adrian V Lee
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA
- Cancer Biology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Tullia C Bruno
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA
| | - Steffi Oesterreich
- Women's Cancer Research Center, UPMC Hillman Cancer Center, Magee-Womens Research Institute, University of Pittsburgh, Pittsburgh, PA, USA.
- Cancer Biology Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
- Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA, USA.
| | - Dario A A Vignali
- Department of Immunology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Tumor Microenvironment Center, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
- Cancer Immunology and Immunotherapy Program, UPMC Hillman Cancer Center, Pittsburgh, PA, USA.
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Dessources K, Ferrando L, Zhou QC, Iasonos A, Abu-Rustum NR, Reis-Filho JS, Riaz N, Zamarin D, Weigelt B. Impact of immune infiltration signatures on prognosis in endometrial carcinoma is dependent on the underlying molecular subtype. Gynecol Oncol 2023; 171:15-22. [PMID: 36804617 PMCID: PMC10040428 DOI: 10.1016/j.ygyno.2023.01.037] [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: 10/28/2022] [Revised: 01/04/2023] [Accepted: 01/30/2023] [Indexed: 02/18/2023]
Abstract
OBJECTIVES Increased numbers of tumor infiltrating lymphocytes (TIL) in endometrial cancer (EC) are associated with improved survival, but it is unclear how this prognostic significance relates to the underlying EC molecular subtype. In this explorative hypothesis-generating study, we sought to define the immune signatures associated with the molecular subtypes of EC (i.e., POLE-mutated, microsatellite unstable (MSI-high), copy number (CN)-low, and CN-high) and to determine their correlation with patient outcomes. METHODS RNA-sequencing and molecular subtype data of 232 primary ECs were obtained from The Cancer Genome Atlas. Deconvolution of bulk gene expression data was performed using single sample Gene Set Enrichment Analysis (ssGSEA) and Cell type Identification By Estimating Relative Subsets Of known RNA Transcripts (CIBERSORT). The association of the resultant immune signatures with overall survival was determined across molecular subtypes. RESULTS Statistically significant differences in enrichment were identified in 16/30 and 6/23 immune gene sets by ssGSEA and CIBERSORT, respectively. Signature of CD8+ cells in ECs of CN-high molecular subtype was associated with improved overall survival by ssGSEA (p = 0.0108), while CD8 signatures did not appear to be prognostic in MSI-high (p = 0.74) or CN-low EC molecular subtypes (p = 0.793). Of all molecular subtypes, CN-high ECs exhibited the lowest levels of CD8+ T cell infiltration. Consistent with antigen-induced T cell activation and exhaustion, enrichment for immunomodulatory receptors was predominantly observed in ECs of MSI-high and POLE-mutated molecular subtypes. CONCLUSIONS Deconvolution of bulk gene expression data can be used to identify populations of immune infiltrated endometrial cancers with improved survival. These data support the existence of unique mechanisms of immune resistance within molecular subgroups of the disease.
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Affiliation(s)
- Kimberly Dessources
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorenzo Ferrando
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Current address: IRCCS - Ospedale Policlinico San Martino, Genova, Italy
| | - Qin C Zhou
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexia Iasonos
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem R Abu-Rustum
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dmitriy Zamarin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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Ma L, Feng Y, Zhou Z. A close look at current γδ T-cell immunotherapy. Front Immunol 2023; 14:1140623. [PMID: 37063836 PMCID: PMC10102511 DOI: 10.3389/fimmu.2023.1140623] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Accepted: 03/08/2023] [Indexed: 04/03/2023] Open
Abstract
Owing to their antitumor and major histocompatibility complex (MHC)-independent capacities, γδ T cells have gained popularity in adoptive T-cell immunotherapy in recent years. However, many unknowns still exist regarding γδ T cells, and few clinical data have been collected. Therefore, this review aims to describe all the main features of the applications of γδ T cells and provide a systematic view of current γδ T-cell immunotherapy. Specifically, this review will focus on how γδ T cells performed in treating cancers in clinics, on the γδ T-cell clinical trials that have been conducted to date, and the role of γδ T cells in the pharmaceutical industry.
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Affiliation(s)
- Ling Ma
- Institute of Molecular Medicine, College of Future Technology, Peking University, Beijing, China
- Research and Development Department, Beijing Dingchengtaiyuan (DCTY) Biotech Co., Ltd., Beijing, China
| | - Yanmin Feng
- Research and Development Department, Beijing Dingchengtaiyuan (DCTY) Biotech Co., Ltd., Beijing, China
| | - Zishan Zhou
- Research and Development Department, Beijing Dingchengtaiyuan (DCTY) Biotech Co., Ltd., Beijing, China
- *Correspondence: Zishan Zhou,
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Defining the Emergence of New Immunotherapy Approaches in Breast Cancer: Role of Myeloid-Derived Suppressor Cells. Int J Mol Sci 2023; 24:ijms24065208. [PMID: 36982282 PMCID: PMC10048951 DOI: 10.3390/ijms24065208] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/24/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
Breast cancer (BC) continues to be the most diagnosed tumor in women and a very heterogeneous disease both inter- and intratumoral, mainly given by the variety of molecular profiles with different biological and clinical characteristics. Despite the advancements in early detection and therapeutic strategies, the survival rate is low in patients who develop metastatic disease. Therefore, it is mandatory to explore new approaches to achieve better responses. In this regard, immunotherapy arose as a promising alternative to conventional treatments due to its ability to modulate the immune system, which may play a dual role in this disease since the relationship between the immune system and BC cells depends on several factors: the tumor histology and size, as well as the involvement of lymph nodes, immune cells, and molecules that are part of the tumor microenvironment. Particularly, myeloid-derived suppressor cell (MDSC) expansion is one of the major immunosuppressive mechanisms used by breast tumors since it has been associated with worse clinical stage, metastatic burden, and poor efficacy of immunotherapies. This review focuses on the new immunotherapies in BC in the last five years. Additionally, the role of MDSC as a therapeutic target in breast cancer will be described.
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Zwager MC, Bense R, Waaijer S, Qiu SQ, Timmer-Bosscha H, de Vries EGE, Schröder CP, van der Vegt B. Assessing the role of tumour-associated macrophage subsets in breast cancer subtypes using digital image analysis. Breast Cancer Res Treat 2023; 198:11-22. [PMID: 36622544 PMCID: PMC9883348 DOI: 10.1007/s10549-022-06859-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 12/29/2022] [Indexed: 01/10/2023]
Abstract
PURPOSE The number of M1-like and M2-like tumour-associated macrophages (TAMs) and their ratio can play a role in breast cancer development and progression. Early clinical trials using macrophage targeting compounds are currently ongoing. However, the most optimal detection method of M1-like and M2-like macrophage subsets and their clinical relevance in breast cancer is still unclear. We aimed to optimize the assessment of TAM subsets in different breast cancer subtypes, and therefore related TAM subset numbers and ratio to clinicopathological characteristics and clinical outcome. METHODS Tissue microarrays of 347 consecutive primary Luminal-A, Luminal-B, HER2-positive and triple-negative tumours of patients with early-stage breast cancer were serially sectioned and immunohistochemically stained for the pan-macrophage marker CD68 and the M2-like macrophage markers CD163, CSF-1R and CD206. TAM numbers were quantified using a digital image analysis algorithm. M1-like macrophage numbers were calculated by subtracting M2-like TAM numbers from the total TAM number. RESULTS M2-like markers CD163 and CSF-1R showed a moderate positive association with each other and with CD68 (r ≥ 0.47), but only weakly with CD206 (r ≤ 0.06). CD68 + , CD163 + and CSF-1R + macrophages correlated with tumour grade in Luminal-B tumours (P < 0.001). Total or subset TAM numbers did not correlate with disease outcome in any breast cancer subtype. CONCLUSION In conclusion, macrophages and their subsets can be detected by means of a panel of TAM markers and are related to unfavourable clinicopathological characteristics in Luminal-B breast cancer. However, their impact on outcome remains unclear. Preferably, this should be determined in prospective series.
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Affiliation(s)
- Mieke C. Zwager
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Rico Bense
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Stijn Waaijer
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Si-Qi Qiu
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Diagnosis and Treatment Center of Breast Diseases, Clinical Research Center, Shantou Central Hospital, Shantou, China
- Guangdong Provincial Key Laboratory for Breast Cancer Diagnosis and Treatment, Shantou University Medical College, Shantou, China
| | - Hetty Timmer-Bosscha
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Elisabeth G. E. de Vries
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Carolien P. Schröder
- Department of Medical Oncology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Medical Oncology, Dutch Cancer Institute, Amsterdam, Netherlands
| | - Bert van der Vegt
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, PO Box 30001, 9700 RB Groningen, The Netherlands
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