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Maciejewski K, Czerwinska P. Scoping Review: Methods and Applications of Spatial Transcriptomics in Tumor Research. Cancers (Basel) 2024; 16:3100. [PMID: 39272958 PMCID: PMC11394603 DOI: 10.3390/cancers16173100] [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: 07/19/2024] [Revised: 08/30/2024] [Accepted: 08/30/2024] [Indexed: 09/15/2024] Open
Abstract
Spatial transcriptomics (ST) examines gene expression within its spatial context on tissue, linking morphology and function. Advances in ST resolution and throughput have led to an increase in scientific interest, notably in cancer research. This scoping study reviews the challenges and practical applications of ST, summarizing current methods, trends, and data analysis techniques for ST in neoplasm research. We analyzed 41 articles published by the end of 2023 alongside public data repositories. The findings indicate cancer biology is an important focus of ST research, with a rising number of studies each year. Visium (10x Genomics, Pleasanton, CA, USA) is the leading ST platform, and SCTransform from Seurat R library is the preferred method for data normalization and integration. Many studies incorporate additional data types like single-cell sequencing and immunohistochemistry. Common ST applications include discovering the composition and function of tumor tissues in the context of their heterogeneity, characterizing the tumor microenvironment, or identifying interactions between cells, including spatial patterns of expression and co-occurrence. However, nearly half of the studies lacked comprehensive data processing protocols, hindering their reproducibility. By recommending greater transparency in sharing analysis methods and adapting single-cell analysis techniques with caution, this review aims to improve the reproducibility and reliability of future studies in cancer research.
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Affiliation(s)
- Kacper Maciejewski
- Undergraduate Research Group "Biobase", Poznan University of Medical Sciences, 61-701 Poznan, Poland
| | - Patrycja Czerwinska
- Undergraduate Research Group "Biobase", Poznan University of Medical Sciences, 61-701 Poznan, Poland
- Department of Cancer Immunology, Poznan University of Medical Sciences, 61-866 Poznan, Poland
- Department of Diagnostics and Cancer Immunology, Greater Poland Cancer Centre, 61-866 Poznan, Poland
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Wang K, Peng B, Xu R, Lu T, Chang X, Shen Z, Shi J, Li M, Wang C, Zhou X, Xu C, Chang H, Zhang L. Comprehensive analysis of PPP4C's impact on prognosis, immune microenvironment, and immunotherapy response in lung adenocarcinoma using single-cell sequencing and multi-omics. Front Immunol 2024; 15:1416632. [PMID: 39026674 PMCID: PMC11254641 DOI: 10.3389/fimmu.2024.1416632] [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: 04/12/2024] [Accepted: 06/17/2024] [Indexed: 07/20/2024] Open
Abstract
Background Elevated PPP4C expression has been associated with poor prognostic implications for patients suffering from lung adenocarcinoma (LUAD). The extent to which PPP4C affects immune cell infiltration in LUAD, as well as the importance of associated genes in clinical scenarios, still requires thorough investigation. Methods In our investigation, we leveraged both single-cell and comprehensive RNA sequencing data, sourced from LUAD patients, in our analysis. This study also integrated datasets of immune-related genes from InnateDB into the framework. Our expansive evaluation employed various analytical techniques; these included pinpointing differentially expressed genes, constructing WGCNA, implementing Cox proportional hazards models. We utilized these methods to investigate the gene expression profiles of PPP4C within the context of LUAD and to clarify its potential prognostic value for patients. Subsequent steps involved validating the observed enhancement of PPP4C expression in LUAD samples through a series of experimental approaches. The array comprised immunohistochemistry staining, Western blotting, quantitative PCR, and a collection of cell-based assays aimed at evaluating the influence of PPP4C on the proliferative and migratory activities of LUAD cells. Results In lung cancer, elevated expression levels of PPP4C were observed, correlating with poorer patient prognoses. Validation of increased PPP4C levels in LUAD specimens was achieved using immunohistochemical techniques. Experimental investigations have substantiated the role of PPP4C in facilitating cellular proliferation and migration in LUAD contexts. Furthermore, an association was identified between the expression of PPP4C and the infiltration of immune cells in these tumors. A prognostic framework, incorporating PPP4C and immune-related genes, was developed and recognized as an autonomous predictor of survival in individuals afflicted with LUAD. This prognostic tool has demonstrated considerable efficacy in forecasting patient survival and their response to immunotherapeutic interventions. Conclusion The involvement of PPP4C in LUAD is deeply intertwined with the tumor's immune microenvironment. PPP4C's over-expression is associated with negative clinical outcomes, promoting both tumor proliferation and spread. A prognostic framework based on PPP4C levels may effectively predict patient prognoses in LUAD, as well as the efficacy of immunotherapy strategy. This research sheds light on the mechanisms of immune interaction in LUAD and proposes a new strategy for treatment.
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Affiliation(s)
- Kaiyu Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Bo Peng
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Ran Xu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Tong Lu
- Department of Thoracic Surgery, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaoyan Chang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Zhiping Shen
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Jiaxin Shi
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Meifeng Li
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chenghao Wang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Xiang Zhou
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Chengyu Xu
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hao Chang
- Department of Thoracic Surgery, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Linyou Zhang
- Department of Thoracic Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, China
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Li Q, Fang J, Liu K, Luo P, Wang X. Multi-omic validation of the cuproptosis-sphingolipid metabolism network: modulating the immune landscape in osteosarcoma. Front Immunol 2024; 15:1424806. [PMID: 38983852 PMCID: PMC11231095 DOI: 10.3389/fimmu.2024.1424806] [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: 04/28/2024] [Accepted: 06/06/2024] [Indexed: 07/11/2024] Open
Abstract
Background The current understanding of the mechanisms by which metal ion metabolism promotes the progression and drug resistance of osteosarcoma remains incomplete. This study aims to elucidate the key roles and mechanisms of genes involved in cuproptosis-related sphingolipid metabolism (cuproptosis-SPGs) in regulating the immune landscape, tumor metastasis, and drug resistance in osteosarcoma cells. Methods This study employed multi-omics approaches to assess the impact of cuproptosis-SPGs on the prognosis of osteosarcoma patients. Lasso regression analysis was utilized to construct a prognostic model, while multivariate regression analysis was applied to identify key core genes and generate risk coefficients for these genes, thereby calculating a risk score for each osteosarcoma patient. Patients were then stratified into high-risk and low-risk groups based on their risk scores. The ESTIMATE and CIBERSORT algorithms were used to analyze the level of immune cell infiltration within these risk groups to construct the immune landscape. Single-cell analysis was conducted to provide a more precise depiction of the expression patterns of cuproptosis-SPGs among immune cell subtypes. Finally, experiments on osteosarcoma cells were performed to validate the role of the cuproptosis-sphingolipid signaling network in regulating cell migration and apoptosis. Results In this study, seven cuproptosis-SPGs were identified and used to construct a prognostic model for osteosarcoma patients. In addition to predicting survival, the model also demonstrated reliability in forecasting the response to chemotherapy drugs. The results showed that a high cuproptosis-sphingolipid metabolism score was closely associated with reduced CD8 T cell infiltration and indicated poor prognosis in osteosarcoma patients. Cellular functional assays revealed that cuproptosis-SPGs regulated the LC3B/ERK signaling pathway, thereby triggering cell death and impairing migration capabilities in osteosarcoma cells. Conclusion The impact of cuproptosis-related sphingolipid metabolism on the survival and migration of osteosarcoma cells, as well as on CD8 T cell infiltration, highlights the potential of targeting copper ion metabolism as a promising strategy for osteosarcoma patients.
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Affiliation(s)
- Qingbiao Li
- Department of Orthopedics, Southern Medical University Pingshan Hospital (Pingshan District Peoples’ Hospital of Shenzhen), Shenzhen, Guangdong, China
| | - Jiarui Fang
- Department of Sport Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, China
| | - Kai Liu
- Department of Sport Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, China
| | - Peng Luo
- Department of Sport Medicine, Huazhong University of Science and Technology Union Shenzhen Hospital (Nanshan Hospital), Shenzhen, China
| | - Xiuzhuo Wang
- Department of Orthopedics, Southern Medical University Pingshan Hospital (Pingshan District Peoples’ Hospital of Shenzhen), Shenzhen, Guangdong, China
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Wen X, Hou J, Qi T, Cheng X, Liao G, Fang S, Xiao S, Qiu L, Wei W. Anoikis resistance regulates immune infiltration and drug sensitivity in clear-cell renal cell carcinoma: insights from multi omics, single cell analysis and in vitro experiment. Front Immunol 2024; 15:1427475. [PMID: 38953023 PMCID: PMC11215044 DOI: 10.3389/fimmu.2024.1427475] [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: 05/03/2024] [Accepted: 06/05/2024] [Indexed: 07/03/2024] Open
Abstract
Background Anoikis is a form of programmed cell death essential for preventing cancer metastasis. In some solid cancer, anoikis resistance can facilitate tumor progression. However, this phenomenon is underexplored in clear-cell renal cell carcinoma (ccRCC). Methods Using SVM machine learning, we identified core anoikis-related genes (ARGs) from ccRCC patient transcriptomic data. A LASSO Cox regression model stratified patients into risk groups, informing a prognostic model. GSVA and ssGSEA assessed immune infiltration, and single-cell analysis examined ARG expression across immune cells. Quantitative PCR and immunohistochemistry validated ARG expression differences between immune therapy responders and non-responders in ccRCC. Results ARGs such as CCND1, CDKN3, PLK1, and BID were key in predicting ccRCC outcomes, linking higher risk with increased Treg infiltration and reduced M1 macrophage presence, indicating an immunosuppressive environment facilitated by anoikis resistance. Single-cell insights showed ARG enrichment in Tregs and dendritic cells, affecting immune checkpoints. Immunohistochemical analysis reveals that ARGs protein expression is markedly elevated in ccRCC tissues responsive to immunotherapy. Conclusion This study establishes a novel anoikis resistance gene signature that predicts survival and immunotherapy response in ccRCC, suggesting that manipulating the immune environment through these ARGs could improve therapeutic strategies and prognostication in ccRCC.
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MESH Headings
- Humans
- Carcinoma, Renal Cell/immunology
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/pathology
- Carcinoma, Renal Cell/drug therapy
- Anoikis/drug effects
- Kidney Neoplasms/immunology
- Kidney Neoplasms/genetics
- Kidney Neoplasms/pathology
- Single-Cell Analysis
- Prognosis
- Gene Expression Regulation, Neoplastic
- Drug Resistance, Neoplasm/genetics
- Tumor Microenvironment/immunology
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Transcriptome
- Cell Line, Tumor
- Biomarkers, Tumor/genetics
- T-Lymphocytes, Regulatory/immunology
- Gene Expression Profiling
- Male
- Multiomics
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Affiliation(s)
- Xiangyang Wen
- The Department of Surgery, Shenzhen Longgang Second People’s Hospital, Shenzhen, China
| | - Jian Hou
- Department of Urology, The University of Hongkong-Shenzhen Hospital, Shenzhen, China
| | - Tiantian Qi
- Department of Bone & Joint Surgery, Peking University Shenzhen Hospital, Shenzhen, China
| | - Xiaobao Cheng
- Department of Urology, The University of Hongkong-Shenzhen Hospital, Shenzhen, China
| | - Guoqiang Liao
- The Department of Surgery, Shenzhen Longgang Second People’s Hospital, Shenzhen, China
| | - Shaohong Fang
- The Department of Surgery, Shenzhen Longgang Second People’s Hospital, Shenzhen, China
| | - Song Xiao
- The Department of Surgery, Shenzhen Longgang Second People’s Hospital, Shenzhen, China
| | - Longlong Qiu
- The Department of Surgery, Shenzhen Longgang Second People’s Hospital, Shenzhen, China
| | - Wanqing Wei
- Department of Urology, Lianshui People’s Hospital of Kangda College Affiliated to Nanjing Medical University, Huaian, China
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Fedele M, Cerchia L, Battista S. Subtype Transdifferentiation in Human Cancer: The Power of Tissue Plasticity in Tumor Progression. Cells 2024; 13:350. [PMID: 38391963 PMCID: PMC10887430 DOI: 10.3390/cells13040350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/08/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024] Open
Abstract
The classification of tumors into subtypes, characterized by phenotypes determined by specific differentiation pathways, aids diagnosis and directs therapy towards targeted approaches. However, with the advent and explosion of next-generation sequencing, cancer phenotypes are turning out to be far more heterogenous than initially thought, and the classification is continually being updated to include more subtypes. Tumors are indeed highly dynamic, and they can evolve and undergo various changes in their characteristics during disease progression. The picture becomes even more complex when the tumor responds to a therapy. In all these cases, cancer cells acquire the ability to transdifferentiate, changing subtype, and adapt to changing microenvironments. These modifications affect the tumor's growth rate, invasiveness, response to treatment, and overall clinical behavior. Studying tumor subtype transitions is crucial for understanding tumor evolution, predicting disease outcomes, and developing personalized treatment strategies. We discuss this emerging hallmark of cancer and the molecular mechanisms involved at the crossroads between tumor cells and their microenvironment, focusing on four different human cancers in which tissue plasticity causes a subtype switch: breast cancer, prostate cancer, glioblastoma, and pancreatic adenocarcinoma.
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Affiliation(s)
- Monica Fedele
- Institute of Experimental Endocrinology and Oncology “G. Salvatore” (IEOS), National Research Council—CNR, 80131 Naples, Italy; (L.C.); (S.B.)
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Chen E, Ling AL, Reardon DA, Chiocca EA. Lessons learned from phase 3 trials of immunotherapy for glioblastoma: Time for longitudinal sampling? Neuro Oncol 2024; 26:211-225. [PMID: 37995317 PMCID: PMC10836778 DOI: 10.1093/neuonc/noad211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2023] Open
Abstract
Glioblastoma (GBM)'s median overall survival is almost 21 months. Six phase 3 immunotherapy clinical trials have recently been published, yet 5/6 did not meet approval by regulatory bodies. For the sixth, approval is uncertain. Trial failures result from multiple factors, ranging from intrinsic tumor biology to clinical trial design. Understanding the clinical and basic science of these 6 trials is compelled by other immunotherapies reaching the point of advanced phase 3 clinical trial testing. We need to understand more of the science in human GBMs in early trials: the "window of opportunity" design may not be best to understand complex changes brought about by immunotherapeutic perturbations of the GBM microenvironment. The convergence of increased safety of image-guided biopsies with "multi-omics" of small cell numbers now permits longitudinal sampling of tumor and biofluids to dissect the complex temporal changes in the GBM microenvironment as a function of the immunotherapy.
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Affiliation(s)
- Ethan Chen
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - Alexander L Ling
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, Massachusetts, USA
| | - David A Reardon
- Center for Neuro-Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - E Antonio Chiocca
- Department of Neurosurgery, Brigham and Women’s Hospital, Boston, Massachusetts, USA
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