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Ma Y, Li J, Xiong C, Sun X, Shen T. Development of a prognostic model for NSCLC based on differential genes in tumour stem cells. Sci Rep 2024; 14:20938. [PMID: 39251710 PMCID: PMC11383933 DOI: 10.1038/s41598-024-71317-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 08/27/2024] [Indexed: 09/11/2024] Open
Abstract
Non-small cell lung cancer (NSCLC) constitutes a significant portion of lung cancers and cytotoxic drugs (e.g. cisplatin) are currently the first-line treatment. However, NSCLC has developed resistance to this drug, which limits the therapeutic effect and thus affects prognosis. NSCLC sc-RNA-seq data were downloaded from the GEO database and Ku Leuven Laboratory for Functional Epigenetics, and bulk RNA-seq data were obtained from the TCGA database. The "Seurat" package was employed for scRNA-seq data processing, and the uniform manifold approximation and projection (UMAP) were applied for downscaling and cluster identification. Use the FindAllMarkers function to find differential genes (DEGs) for tumor stem cells. Then, we performed univariate regression analyses on the DEGs to identify potential prognostic genes. We created a machine learning framework based on potential prognostic genes, which combines 10 machine learning methods and their 101 combinations to get the optimal prognostic risk model. The model was evaluated in the training set and validation set. A nomogram was developed to provide physicians with a quantitative tool for prognosis prediction. Finally, we evaluated the expression and functionality of SLC2A1. We discovered 22 cell clusters containing 218379 cells by examining single-cell RNA sequencing datasets (GSE148071, KU_lom, GSE131907, GSE136246, GSE127465). Tumour cells were isolated for subpopulation analysis and 162 differential genes from SOX2_cancer were obtained. After univariate Cox analysis, we found 23 genes with prognostic potential prognostic value and utilized them to develop 101‑combination machine learning computational framework. We eventually picked the best performing 'StepCox[both] + RSF', which includes 8 genes. The model has a relatively high prediction accuracy in both TCGA and GEO datasets. In in vitro investigations, targeted suppression of the SLC2A1 gene resulted in significant reductions in proliferation, invasion and migration in A549 cells. In addition, a significant reduction in cisplatin resistance was seen in A549/DDP cells. The outcomes demonstrated the precision and credibility of the prognostic model for NSCLC, highlighting its potential significance in the treatment and prognosis of individuals affected by this disease. SLC2A1 may become a promising prognostic marker and a potential therapeutic target, offering valuable insights to inform clinical treatment decisions.
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Affiliation(s)
- Yuqi Ma
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Jiawei Li
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Chunping Xiong
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xiaoluo Sun
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Tao Shen
- School of Basic Medical Sciences, Chengdu University of Traditional Chinese Medicine, Chengdu, China.
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2
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Zhu Y, Wu X, Zhang Y, Gu J, Zhou R, Guo Z. Single cell transcriptomic analysis reveals tumor immune infiltration by NK cells gene signature in lung adenocarcinoma. Heliyon 2024; 10:e33928. [PMID: 39071697 PMCID: PMC11283104 DOI: 10.1016/j.heliyon.2024.e33928] [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: 11/03/2023] [Revised: 06/28/2024] [Accepted: 06/30/2024] [Indexed: 07/30/2024] Open
Abstract
Background Natural Killer (NK) cells are vital components of the innate immune system, crucial for combating infections and tumor growth, making them pivotal in cancer prognosis and immunotherapy. We sought to understand the diverse characteristics of NK cells within lung adenocarcinoma (LUAD) by conducting single-cell RNA sequencing analyses. Methods Using the scRNA-seq dataset for multiple primary lung cancers (MPLCs), we examined two major NK cell groups, NK1 and NK2, comparing the expression profiles of 422 differentially expressed NK signature genes. We identified eight genes (SPON2, PLEKHG3, CAMK2N1, RAB27B, CTBP2, EFHD2, GOLM1, and PLOD1) that distinguish NK1 from NK2 cells. A prognostic signature, the NK gene signature (NKGS) score, was established through LASSO Cox regression. High NKGS scores were linked to poorer overall survival in TCGA-LUAD patients and consistently validated in other datasets (GSE31210 and GSE14814). Results Functional analysis revealed an enrichment of genes related to the TGF-β signaling pathway in the high NKGS score group. Moreover, a high NKGS score correlated with an immunosuppressive tumor microenvironment (TME) driven by immune evasion mechanisms. We also observed reduced T-cell receptor (TCR) repertoire diversity in the high-risk NKGS group, indicating a negative association between inflammation and risk score. Conclusion This study introduced the innovative NKGS score, differentiating NK1 from NK2 cells. High NKGS scores were associated with the TGF-β pathway and provided insights into LUAD prognosis and immune activities.
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Affiliation(s)
- Yimin Zhu
- Department of Pulmonary and Critical Care Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xiuhua Wu
- Department of Pulmonary and Critical Care Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunjiao Zhang
- Department of Pulmonary and Critical Care Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jie Gu
- Department of Pulmonary and Critical Care Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Rongwei Zhou
- Department of Pulmonary and Critical Care Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhong Guo
- Department of Pulmonary and Critical Care Medicine, Shanghai Sixth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
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3
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Shantaram D, Hoyd R, Blaszczak AM, Antwi L, Jalilvand A, Wright VP, Liu J, Smith AJ, Bradley D, Lafuse W, Liu Y, Williams NF, Snyder O, Wheeler C, Needleman B, Brethauer S, Noria S, Renton D, Perry KA, Nagareddy P, Wozniak D, Mahajan S, Rana PSJB, Pietrzak M, Schlesinger LS, Spakowicz DJ, Hsueh WA. Obesity-associated microbiomes instigate visceral adipose tissue inflammation by recruitment of distinct neutrophils. Nat Commun 2024; 15:5434. [PMID: 38937454 PMCID: PMC11211470 DOI: 10.1038/s41467-024-48935-5] [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: 12/05/2022] [Accepted: 05/17/2024] [Indexed: 06/29/2024] Open
Abstract
Neutrophils are increasingly implicated in chronic inflammation and metabolic disorders. Here, we show that visceral adipose tissue (VAT) from individuals with obesity contains more neutrophils than in those without obesity and is associated with a distinct bacterial community. Exploring the mechanism, we gavaged microbiome-depleted mice with stool from patients with and without obesity during high-fat or normal diet administration. Only mice receiving high-fat diet and stool from subjects with obesity show enrichment of VAT neutrophils, suggesting donor microbiome and recipient diet determine VAT neutrophilia. A rise in pro-inflammatory CD4+ Th1 cells and a drop in immunoregulatory T cells in VAT only follows if there is a transient spike in neutrophils. Human VAT neutrophils exhibit a distinct gene expression pattern that is found in different human tissues, including tumors. VAT neutrophils and bacteria may be a novel therapeutic target for treating inflammatory-driven complications of obesity, including insulin resistance and colon cancer.
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Affiliation(s)
- Dharti Shantaram
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA
| | - Rebecca Hoyd
- Pelotonia Institute for Immuno-Oncology at The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, 43210, USA
| | - Alecia M Blaszczak
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA
| | - Linda Antwi
- Pelotonia Institute for Immuno-Oncology at The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, 43210, USA
| | - Anahita Jalilvand
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA
| | - Valerie P Wright
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA
| | - Joey Liu
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA
| | - Alan J Smith
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA
| | - David Bradley
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA
| | - William Lafuse
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA
| | - YunZhou Liu
- Pelotonia Institute for Immuno-Oncology at The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, 43210, USA
| | - Nyelia F Williams
- Pelotonia Institute for Immuno-Oncology at The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, 43210, USA
| | - Owen Snyder
- Pelotonia Institute for Immuno-Oncology at The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, 43210, USA
| | - Caroline Wheeler
- Pelotonia Institute for Immuno-Oncology at The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, 43210, USA
| | - Bradley Needleman
- Center for Minimally Invasive Surgery, Department of General Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Stacy Brethauer
- Center for Minimally Invasive Surgery, Department of General Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Sabrena Noria
- Center for Minimally Invasive Surgery, Department of General Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - David Renton
- Center for Minimally Invasive Surgery, Department of General Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Kyle A Perry
- Center for Minimally Invasive Surgery, Department of General Surgery, The Ohio State University, Columbus, OH, 43210, USA
| | - Prabha Nagareddy
- Department of Internal Medicine, Cardiovascular Section University of Oklahoma Health Sciences Center (OUHSC), Oklahoma City, OK, 73117, USA
| | - Daniel Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA
| | - Sahil Mahajan
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA
| | - Pranav S J B Rana
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, 43210, USA
| | - Maciej Pietrzak
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, 43210, USA
| | - Larry S Schlesinger
- Host Pathogen Interactions Program, Texas Biomedical Research Institute, San Antonio, TX, 78227, USA
| | - Daniel J Spakowicz
- Pelotonia Institute for Immuno-Oncology at The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, 43210, USA.
| | - Willa A Hsueh
- Diabetes and Metabolism Research Center, Division of Endocrinology, Diabetes & Metabolism, Department of Internal Medicine, Wexner Medical Center at The Ohio State University, Columbus, OH, 43210, USA.
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Li J, Choi J, Cheng X, Ma J, Pema S, Sanes JR, Mardon G, Frankfort BJ, Tran NM, Li Y, Chen R. Comprehensive single-cell atlas of the mouse retina. iScience 2024; 27:109916. [PMID: 38812536 PMCID: PMC11134544 DOI: 10.1016/j.isci.2024.109916] [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: 02/19/2024] [Revised: 03/18/2024] [Accepted: 05/03/2024] [Indexed: 05/31/2024] Open
Abstract
Single-cell RNA sequencing (scRNA-seq) has advanced our understanding of cellular heterogeneity by characterizing cell types across tissues and species. While several mouse retinal scRNA-seq datasets exist, each dataset is either limited in cell numbers or focused on specific cell classes, thereby hindering comprehensive gene expression analysis across all retina types. To fill the gap, we generated the largest retinal scRNA-seq dataset to date, comprising approximately 190,000 single cells from C57BL/6J mouse retinas, enriched for rare population cells via antibody-based magnetic cell sorting. Integrating this dataset with public datasets, we constructed the Mouse Retina Cell Atlas (MRCA) for wild-type mice, encompassing over 330,000 cells, characterizing 12 major classes and 138 cell types. The MRCA consolidates existing knowledge, identifies new cell types, and is publicly accessible via CELLxGENE, UCSC Cell Browser, and the Broad Single Cell Portal, providing a user-friendly resource for the mouse retina research community.
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Affiliation(s)
- Jin Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jongsu Choi
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Xuesen Cheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Justin Ma
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shahil Pema
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02130, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX 77030, USA
- Departments of Ophthalmology and Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Benjamin J. Frankfort
- Departments of Ophthalmology and Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nicholas M. Tran
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
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5
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Piovesan D, de Groot AE, Cho S, Anderson AE, Ray RD, Patnaik A, Foster PG, Mitchell CG, Lopez Espinoza AY, Zhu WS, Stagnaro CE, Singh H, Zhao X, Seitz L, Walker NP, Walters MJ, Sivick KE. Fc-Silent Anti-TIGIT Antibodies Potentiate Antitumor Immunity without Depleting Regulatory T Cells. Cancer Res 2024; 84:1978-1995. [PMID: 38635895 DOI: 10.1158/0008-5472.can-23-2455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 02/02/2024] [Accepted: 04/02/2024] [Indexed: 04/20/2024]
Abstract
T-cell immunoreceptor with immunoglobulin and immunoreceptor tyrosine-based inhibitory motif domains (TIGIT) is an inhibitory receptor on immune cells that outcompetes an activating receptor, CD226, for shared ligands. Tumor-infiltrating lymphocytes express TIGIT and CD226 on regulatory T cells (Treg) and on CD8+ T cells with tumor-reactive or exhausted phenotypes, supporting the potential of therapeutically targeting TIGIT to enhance antitumor immunity. To optimize the efficacy of therapeutic antibodies against TIGIT, it is necessary to understand IgG Fc (Fcγ) receptor binding for therapeutic benefit. In this study, we showed that combining Fc-enabled (Fce) or Fc-silent (Fcs) anti-TIGIT with antiprogrammed cell death protein 1 in mice resulted in enhanced control of tumors by differential mechanisms: Fce anti-TIGIT promoted the depletion of intratumoral Treg, whereas Fcs anti-TIGIT did not. Despite leaving Treg numbers intact, Fcs anti-TIGIT potentiated the activation of tumor-specific exhausted CD8+ populations in a lymph node-dependent manner. Fce anti-TIGIT induced antibody-dependent cell-mediated cytotoxicity against human Treg in vitro, and significant decreases in Treg were measured in the peripheral blood of patients with phase I solid tumor cancer treated with Fce anti-TIGIT. In contrast, Fcs anti-TIGIT did not deplete human Treg in vitro and was associated with anecdotal objective clinical responses in two patients with phase I solid tumor cancer whose peripheral Treg frequencies remained stable on treatment. Collectively, these data provide evidence for pharmacologic activity and antitumor efficacy of anti-TIGIT antibodies lacking the ability to engage Fcγ receptor. SIGNIFICANCE Fcs-silent anti-TIGIT antibodies enhance the activation of tumor-specific pre-exhausted T cells and promote antitumor efficacy without depleting T regulatory cells.
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6
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Tian J, Bai X, Quek C. Single-Cell Informatics for Tumor Microenvironment and Immunotherapy. Int J Mol Sci 2024; 25:4485. [PMID: 38674070 PMCID: PMC11050520 DOI: 10.3390/ijms25084485] [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: 03/08/2024] [Revised: 04/12/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Cancer comprises malignant cells surrounded by the tumor microenvironment (TME), a dynamic ecosystem composed of heterogeneous cell populations that exert unique influences on tumor development. The immune community within the TME plays a substantial role in tumorigenesis and tumor evolution. The innate and adaptive immune cells "talk" to the tumor through ligand-receptor interactions and signaling molecules, forming a complex communication network to influence the cellular and molecular basis of cancer. Such intricate intratumoral immune composition and interactions foster the application of immunotherapies, which empower the immune system against cancer to elicit durable long-term responses in cancer patients. Single-cell technologies have allowed for the dissection and characterization of the TME to an unprecedented level, while recent advancements in bioinformatics tools have expanded the horizon and depth of high-dimensional single-cell data analysis. This review will unravel the intertwined networks between malignancy and immunity, explore the utilization of computational tools for a deeper understanding of tumor-immune communications, and discuss the application of these approaches to aid in diagnosis or treatment decision making in the clinical setting, as well as the current challenges faced by the researchers with their potential future improvements.
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Affiliation(s)
| | | | - Camelia Quek
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW 2006, Australia; (J.T.); (X.B.)
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7
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Deben C, Boullosa LF, Fortes FR, De La Hoz EC, Le Compte M, Seghers S, Peeters M, Vanlanduit S, Lin A, Dijkstra KK, Van Schil P, Hendriks JMH, Prenen H, Roeyen G, Lardon F, Smits E. Auranofin repurposing for lung and pancreatic cancer: low CA12 expression as a marker of sensitivity in patient-derived organoids, with potentiated efficacy by AKT inhibition. J Exp Clin Cancer Res 2024; 43:88. [PMID: 38515178 PMCID: PMC10958863 DOI: 10.1186/s13046-024-03012-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/14/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND This study explores the repurposing of Auranofin (AF), an anti-rheumatic drug, for treating non-small cell lung cancer (NSCLC) adenocarcinoma and pancreatic ductal adenocarcinoma (PDAC). Drug repurposing in oncology offers a cost-effective and time-efficient approach to developing new cancer therapies. Our research focuses on evaluating AF's selective cytotoxicity against cancer cells, identifying RNAseq-based biomarkers to predict AF response, and finding the most effective co-therapeutic agents for combination with AF. METHODS Our investigation employed a comprehensive drug screening of AF in combination with eleven anticancer agents in cancerous PDAC and NSCLC patient-derived organoids (n = 7), and non-cancerous pulmonary organoids (n = 2). Additionally, we conducted RNA sequencing to identify potential biomarkers for AF sensitivity and experimented with various drug combinations to optimize AF's therapeutic efficacy. RESULTS The results revealed that AF demonstrates a preferential cytotoxic effect on NSCLC and PDAC cancer cells at clinically relevant concentrations below 1 µM, sparing normal epithelial cells. We identified Carbonic Anhydrase 12 (CA12) as a significant RNAseq-based biomarker, closely associated with the NF-κB survival signaling pathway, which is crucial in cancer cell response to oxidative stress. Our findings suggest that cancer cells with low CA12 expression are more susceptible to AF treatment. Furthermore, the combination of AF with the AKT inhibitor MK2206 was found to be particularly effective, exhibiting potent and selective cytotoxic synergy, especially in tumor organoid models classified as intermediate responders to AF, without adverse effects on healthy organoids. CONCLUSION Our research offers valuable insights into the use of AF for treating NSCLC and PDAC. It highlights AF's cancer cell selectivity, establishes CA12 as a predictive biomarker for AF sensitivity, and underscores the enhanced efficacy of AF when combined with MK2206 and other therapeutics. These findings pave the way for further exploration of AF in cancer treatment, particularly in identifying patient populations most likely to benefit from its use and in optimizing combination therapies for improved patient outcomes.
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Affiliation(s)
- Christophe Deben
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium.
| | - Laurie Freire Boullosa
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | - Felicia Rodrigues Fortes
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | | | - Maxim Le Compte
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | - Sofie Seghers
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | - Marc Peeters
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | | | - Abraham Lin
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
- Plasma Lab for Applications in Sustainability and Medicine ANTwerp (PLASMANT), University of Antwerp, Wilrijk, Belgium
| | - Krijn K Dijkstra
- Department of Molecular Oncology and Immunology, the Netherlands Cancer Institute - Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Paul Van Schil
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
- Department of Thoracic and Vascular Surgery, Antwerp University Hospital, Edegem, Belgium
| | - Jeroen M H Hendriks
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
- Department of Thoracic and Vascular Surgery, Antwerp University Hospital, Edegem, Belgium
| | - Hans Prenen
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
- Department of Oncology, Multidisciplinary Oncological Center Antwerp, Antwerp University Hospital, Antwerp, Belgium
| | - Geert Roeyen
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
- Department of Hepatobiliary Transplantation and Endocrine Surgery, University Hospital Antwerp (UZA), Edegem, Belgium
| | - Filip Lardon
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
| | - Evelien Smits
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, Wilrijk, Belgium
- Center for Cell Therapy and Regenerative Medicine, Antwerp University Hospital, Edegem, Belgium
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8
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Smith NJ, Reddin I, Policelli P, Oh S, Zainal N, Howes E, Jenkins B, Tracy I, Edmond M, Sharpe B, Amendra D, Zheng K, Egawa N, Doorbar J, Rao A, Mahadevan S, Carpenter MA, Harris RS, Ali S, Hanley C, Buisson R, King E, Thomas GJ, Fenton TR. Differentiation signals induce APOBEC3A expression via GRHL3 in squamous epithelia and squamous cell carcinoma. RESEARCH SQUARE 2024:rs.3.rs-3997426. [PMID: 38496447 PMCID: PMC10942551 DOI: 10.21203/rs.3.rs-3997426/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Two APOBEC (apolipoprotein-B mRNA editing enzyme catalytic polypeptide-like) DNA cytosine deaminase enzymes (APOBEC3A and APOBEC3B) generate somatic mutations in cancer, driving tumour development and drug resistance. Here we used single cell RNA sequencing to study APOBEC3A and APOBEC3B expression in healthy and malignant mucosal epithelia, validating key observations with immunohistochemistry, spatial transcriptomics and functional experiments. Whereas APOBEC3B is expressed in keratinocytes entering mitosis, we show that APOBEC3A expression is confined largely to terminally differentiating cells and requires Grainyhead-like transcription factor 3 (GRHL3). Thus, in normal tissue, neither deaminase appears to be expressed at high levels during DNA replication, the cell cycle stage associated with APOBEC-mediated mutagenesis. In contrast, we show that in squamous cell carcinoma tissues, there is expansion of GRHL3 expression and activity to a subset of cells undergoing DNA replication and concomitant extension of APOBEC3A expression to proliferating cells. These findings indicate a mechanism for acquisition of APOBEC3A mutagenic activity in tumours.
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Affiliation(s)
- Nicola J. Smith
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- School of Biosciences, University of Kent, UK
| | - Ian Reddin
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Bio-R Bioinformatics Research Facility, Faculty of Medicine, University of Southampton, UK
| | - Paige Policelli
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Sunwoo Oh
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Nur Zainal
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Emma Howes
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Benjamin Jenkins
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Ian Tracy
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Mark Edmond
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Benjamin Sharpe
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Damian Amendra
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Ke Zheng
- Department of Pathology, University of Cambridge, UK
| | | | - John Doorbar
- Department of Pathology, University of Cambridge, UK
| | - Anjali Rao
- Gilead Sciences, Research Department, 324 Lakeside Dr. Foster City, CA 94404, USA
| | - Sangeetha Mahadevan
- Gilead Sciences, Research Department, 324 Lakeside Dr. Foster City, CA 94404, USA
| | - Michael A. Carpenter
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX 78229, USA
- Howard Hughes Medical Institute, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Simak Ali
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, UK
| | - Christopher Hanley
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Rémi Buisson
- Department of Biological Chemistry, School of Medicine, University of California Irvine, Irvine, CA, USA
| | - Emma King
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
| | - Gareth J. Thomas
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
| | - Tim R. Fenton
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, UK
- Institute for Life Sciences, University of Southampton, UK
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9
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Li J, Choi J, Cheng X, Ma J, Pema S, Sanes JR, Mardon G, Frankfort BJ, Tran NM, Li Y, Chen R. Comprehensive single-cell atlas of the mouse retina. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.577060. [PMID: 38328114 PMCID: PMC10849744 DOI: 10.1101/2024.01.24.577060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Single-cell RNA sequencing (scRNA-seq) has advanced our understanding of cellular heterogeneity at the single-cell resolution by classifying and characterizing cell types in multiple tissues and species. While several mouse retinal scRNA-seq reference datasets have been published, each dataset either has a relatively small number of cells or is focused on specific cell classes, and thus is suboptimal for assessing gene expression patterns across all retina types at the same time. To establish a unified and comprehensive reference for the mouse retina, we first generated the largest retinal scRNA-seq dataset to date, comprising approximately 190,000 single cells from C57BL/6J mouse whole retinas. This dataset was generated through the targeted enrichment of rare population cells via antibody-based magnetic cell sorting. By integrating this new dataset with public datasets, we conducted an integrated analysis to construct the Mouse Retina Cell Atlas (MRCA) for wild-type mice, which encompasses over 330,000 single cells. The MRCA characterizes 12 major classes and 138 cell types. It captured consensus cell type characterization from public datasets and identified additional new cell types. To facilitate the public use of the MRCA, we have deposited it in CELLxGENE, UCSC Cell Browser, and the Broad Single Cell Portal for visualization and gene expression exploration. The comprehensive MRCA serves as an easy-to-use, one-stop data resource for the mouse retina communities.
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Affiliation(s)
- Jin Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Jongsu Choi
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Xuesen Cheng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Justin Ma
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Shahil Pema
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Joshua R. Sanes
- Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02130, USA
| | - Graeme Mardon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, Texas 77030, USA
- Departments of Ophthalmology and Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Benjamin J. Frankfort
- Departments of Ophthalmology and Neuroscience, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Nicholas M. Tran
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Yumei Li
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Rui Chen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA
- Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas 77030, USA
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10
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Thorlacius-Ussing J, Jensen C, Nissen NI, Cox TR, Kalluri R, Karsdal M, Willumsen N. The collagen landscape in cancer: profiling collagens in tumors and in circulation reveals novel markers of cancer-associated fibroblast subtypes. J Pathol 2024; 262:22-36. [PMID: 37728068 DOI: 10.1002/path.6207] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 07/07/2023] [Accepted: 08/18/2023] [Indexed: 09/21/2023]
Abstract
Cancer-associated fibroblasts (CAFs) deposit and remodel collagens in the tumor stroma, impacting cancer progression and efficacy of interventions. CAFs are the focus of new therapeutics with the aim of normalizing the tumor microenvironment. To do this, a better understanding of CAF heterogeneity and collagen composition in cancer is needed. In this study, we sought to profile the expression of collagens at multiple levels with the goal of identifying cancer biomarkers. We investigated the collagen expression pattern in various cell types and CAF subtypes in a publicly available single-cell RNA sequencing (RNA-seq) dataset of pancreatic ductal adenocarcinoma. Next, we investigated the collagen expression profile in tumor samples across cancer types from The Cancer Genome Atlas (TCGA) database and evaluated if specific patterns of collagen expression were associated with prognosis. Finally, we profiled circulating collagen peptides using a panel of immunoassays to measure collagen fragments in the serum of cancer patients. We found that pancreatic stellate cells and fibroblasts were the primary producers of collagens in the pancreas. COL1A1, COL3A1, COL5A1, COL6A1 were expressed in all CAF subtypes, whereas COL8A1, COL10A1, COL11A1, COL12A1 were specific to myofibroblast CAFs (myCAF) and COL14A1 specific to inflammatory CAFs (iCAF). In TCGA database, myCAF collagens COL10A1 and COL11A1 were elevated across solid tumor types, and multiple associations between high expression and worse survival were found. Finally, circulating collagen biomarkers were elevated in the serum of patients with cancer relative to healthy controls with COL11A1 (myCAF) having the best diagnostic accuracy of the markers measured. In conclusion, CAFs express a noncanonical collagen profile with specific collagen subtypes associated with iCAFs and myCAFs in PDAC. These collagens are deregulated at the cellular, tumor, and systemic levels across different solid tumors and associate with survival. These findings could lead to new discoveries such as novel biomarkers and therapeutic targets. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Jeppe Thorlacius-Ussing
- Department of Biomedical Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, København N, Denmark
- Biomarkers & Research, Nordic Bioscience A/S, Herlev, Denmark
| | | | - Neel I Nissen
- Biomarkers & Research, Nordic Bioscience A/S, Herlev, Denmark
| | - Thomas R Cox
- Matrix and Metastasis Lab, Cancer Ecosystems Program, Garvan Institute of Medical Research and The Kinghorn Cancer Centre, Darlinghurst, NSW, Australia
- School of Clinical Medicine, UNSW Medicine & Health, UNSW Sydney, Sydney, NSW, Australia
| | - Raghu Kalluri
- Department of Cancer Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Morten Karsdal
- Biomarkers & Research, Nordic Bioscience A/S, Herlev, Denmark
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11
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Nash A, Creaney J. Genomic Landscape of Pleural Mesothelioma and Therapeutic Aftermaths. Curr Oncol Rep 2023; 25:1515-1522. [PMID: 38015374 PMCID: PMC10728264 DOI: 10.1007/s11912-023-01479-1] [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] [Accepted: 11/13/2023] [Indexed: 11/29/2023]
Abstract
PURPOSE OF REVIEW In this article, we provide a comprehensive analysis of recent progress in the genetic characterisation of pleural mesothelioma, and the translation of these findings to clinical practice. RECENT FINDINGS Advancements in sequencing technology have allowed the identification of driver mutations and improved our understanding of how these mutations may shape the mesothelioma tumour microenvironment. However, the identification of frequently mutated regions including CDKN2A, BAP1 and NF2 have, to date, not yet yielded targeted therapy options that outperform standard chemo- and immunotherapies. Similarly, the association between mutational profile and the immune microenvironment or immunotherapy response is not well characterised. Further research into the link between tumour mutational profile and response to therapy is critical for identifying targetable vulnerabilities and stratifying patients for therapy.
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Affiliation(s)
- Alistair Nash
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Australia
- Medical School, University of Western Australia, Perth, Australia
| | - Jenette Creaney
- National Centre for Asbestos Related Diseases, University of Western Australia, Perth, Australia.
- Medical School, University of Western Australia, Perth, Australia.
- Institute for Respiratory Health, Perth, Australia.
- Department for Respiratory Medicine, Sir Charles Gairdner Hospital, Perth, Australia.
- The University of Western Australia, Level 5, Harry Perkins Building, QQ Block, QEII Medical Centre, 6 Verdun St., Nedlands, WA, 6009, Australia.
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12
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Sumitomo R, Menju T, Shimazu Y, Toyazaki T, Chiba N, Miyamoto H, Hirayama Y, Nishikawa S, Tanaka S, Yutaka Y, Yamada Y, Nakajima D, Ohsumi A, Hamaji M, Sato A, Yoshizawa A, Huang C, Haga H, Date H. M2-like tumor-associated macrophages promote epithelial-mesenchymal transition through the transforming growth factor β/Smad/zinc finger e-box binding homeobox pathway with increased metastatic potential and tumor cell proliferation in lung squamous cell carcinoma. Cancer Sci 2023; 114:4521-4534. [PMID: 37806311 PMCID: PMC10728010 DOI: 10.1111/cas.15987] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/18/2023] [Accepted: 09/19/2023] [Indexed: 10/10/2023] Open
Abstract
Epithelial-mesenchymal transition (EMT) promotes primary tumor progression toward a metastatic state. The role of tumor-associated macrophages (TAMs) in inducing EMT in lung squamous cell carcinoma (LUSC) remains unclear. We aimed to clarify the significance of TAMs in relation to EMT in LUSC. We collected 221 LUSC specimens from patients who had undergone surgery. Immunohistochemistry was performed to evaluate M1-like and M2-like TAM distribution and EMT by E-cadherin and vimentin staining. Human LUSC cell lines (H226 and EBC-1) and a human monocyte cell line (THP-1) were used for in vitro experiments. M2-like polarization of TAMs and EMT marker expression in LUSC cells were evaluated by western blotting. The biological behavior of LUSC cells was evaluated by migration, invasion, and cell proliferation assays. Immunohistochemical analysis showed that 166 (75.1%) tumors were E-cadherin-positive and 44 (19.9%) were vimentin-positive. M2-like TAM density in the tumor stroma was significantly associated with vimentin positivity and worse overall survival. Western blotting demonstrated higher levels of CD163, CD206, vascular endothelial growth factor, and transforming growth factor beta 1 (TGF-β1) in TAMs versus unstimulated macrophages. Furthermore, increased TGF-β1 secretion from TAMs was confirmed by ELISA. TAM-co-cultured H226 and EBC-1 cells exhibited EMT (decreased E-cadherin, increased vimentin). Regarding EMT-activating transcriptional factors, phosphorylated Smad3 and ZEB-family proteins were higher in TAM-co-cultured LUSC cells than in parental cells. TAM-co-cultured H226 and EBC-1 cells demonstrated enhanced migration and invasion capabilities and improved proliferation. Overall, the present study suggests that TAMs can induce EMT with increased metastatic potential and tumor cell proliferation in LUSC.
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Affiliation(s)
- Ryota Sumitomo
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
- Department of Thoracic SurgeryTazuke Kofukai Medical Research Institute, Kitano HospitalOsakaJapan
| | - Toshi Menju
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Yumeta Shimazu
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Toshiya Toyazaki
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Naohisa Chiba
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Hideaki Miyamoto
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Yutaka Hirayama
- Department of Respiratory Medicine, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Shigeto Nishikawa
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Satona Tanaka
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Yojiro Yutaka
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Yoshito Yamada
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Daisuke Nakajima
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Akihiro Ohsumi
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Masatsugu Hamaji
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Atsuyasu Sato
- Department of Respiratory Medicine, Graduate School of MedicineKyoto UniversityKyotoJapan
| | - Akihiko Yoshizawa
- Department of Diagnostic PathologyKyoto University HospitalKyotoJapan
| | - Cheng‐Long Huang
- Department of Thoracic SurgeryTazuke Kofukai Medical Research Institute, Kitano HospitalOsakaJapan
| | - Hironori Haga
- Department of Diagnostic PathologyKyoto University HospitalKyotoJapan
| | - Hiroshi Date
- Department of Thoracic Surgery, Graduate School of MedicineKyoto UniversityKyotoJapan
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13
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Palermo B, Franzese O, Frisullo G, D'Ambrosio L, Panetta M, Campo G, D'Andrea D, Sperduti I, De Nicola F, Goeman F, Gallina F, Visca P, Facciolo F, Nisticò P. CD28/PD1 co-expression: dual impact on CD8 + T cells in peripheral blood and tumor tissue, and its significance in NSCLC patients' survival and ICB response. J Exp Clin Cancer Res 2023; 42:287. [PMID: 37898752 PMCID: PMC10612243 DOI: 10.1186/s13046-023-02846-3] [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: 07/27/2023] [Accepted: 09/29/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND Immune checkpoint blockade (ICB) has significantly prolonged survival of non-small cell lung cancer (NSCLC) patients, although most patients develop mechanisms of resistance. Recently single-cell RNA-sequencing (scRNA-Seq) revealed a huge T-cell phenotypic and (dys)functional state variability. Accordingly, T-cell exhaustion is recognized as a functional adaptation, with a dynamic progression from a long-lived "pre-exhausted stem-like progenitor" to a "terminally exhausted" state. In this scenario it is crucial to understand the complex interplay between co-stimulatory and inhibitory molecules in CD8+ T-cell functionality. METHODS To gain a baseline landscape of the composition, functional states, and transcriptomic signatures predictive of prognosis, we analyzed CD8+ T-cell subsets characterized by the presence/absence of PD1 and CD28 from periphery, adjacent non-tumor tissue and tumor site of a cohort of treatment-naïve NSCLC patients, by integrated multiparametric flow cytometry, targeted multi-omic scRNA-seq analyses, and computational pipelines. RESULTS Despite the increased PD1 levels, an improved PD1+CD28+ T-cell polyfunctionality was observed with the transition from periphery to tumor site, associated with lack of TIGIT, TIM-3 and LAG-3, but not with Ag-experienced-marker CD11a. Differently from CD28+ T cells, the increased PD1 levels in the tumor were associated with reduced functionality in PD1+CD28- T cells. CD11ahigh, although expressed only in a small fraction of this subset, still sustained its functionality. Absence of TIGIT, TIM-3 and CTLA-4, alone or combined, was beneficial to CD28- T cells. Notably, we observed distinct TRM phenotypes in the different districts, with CD28+ T cells more capable of producing TGFβ in the periphery, potentially contributing to elevated CD103 levels. In contrast CD28- TRM mainly produced CXCL13 within the tumor. ScRNA-seq revealed 5 different clusters for each of the two subsets, with distinctive transcriptional profiles in the three districts. By interrogating the TCGA dataset of patients with lung adenocarcinoma (LUAD) and metastatic NSCLC treated with atezolizumab, we found signatures of heterogeneous TRM and "pre-exhausted" long-lived effector memory CD8+ T cells associated with improved response to ICB only in the presence of CD28. CONCLUSIONS Our findings identify signatures able to stratify survival of LUAD patients and predict ICB response in advanced NSCLC. CD28 is advocated as a key determinant in the signatures identified, in both periphery and tumor site, thus likely providing feasible biomarkers of ICB response.
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Affiliation(s)
- Belinda Palermo
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Ornella Franzese
- Department of Systems Medicine, University of Rome "Tor Vergata", Rome, Italy
| | - Giuseppe Frisullo
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Lorenzo D'Ambrosio
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Mariangela Panetta
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Giulia Campo
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Daniel D'Andrea
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Isabella Sperduti
- Biostatistics and Scientific Direction, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | | | - Frauke Goeman
- SAFU Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Filippo Gallina
- Thoracic-Surgery Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Paolo Visca
- Pathology Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Francesco Facciolo
- Thoracic-Surgery Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy
| | - Paola Nisticò
- Tumor Immunology and Immunotherapy Unit, IRCCS-Regina Elena National Cancer Institute, Rome, Italy.
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14
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Meira DD, de Castro e Caetano MC, Casotti MC, Zetum ASS, Gonçalves AFM, Moreira AR, de Oliveira AH, Pesente F, Santana GM, de Almeida Duque D, Pereira GSC, de Castro GDSC, Pavan IP, Chagas JPS, Bourguignon JHB, de Oliveira JR, Barbosa KRM, Altoé LSC, Louro LS, Merigueti LP, Alves LNR, Machado MRR, Roque MLRO, Prates PS, de Paula Segáua SH, dos Santos Uchiya T, Louro TES, Daleprane VE, Guaitolini YM, Vicente CR, dos Reis Trabach RS, de Araújo BC, dos Santos EDVW, de Paula F, Lopes TJS, de Carvalho EF, Louro ID. Prognostic Factors and Markers in Non-Small Cell Lung Cancer: Recent Progress and Future Challenges. Genes (Basel) 2023; 14:1906. [PMID: 37895255 PMCID: PMC10606762 DOI: 10.3390/genes14101906] [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: 09/01/2023] [Revised: 09/29/2023] [Accepted: 10/01/2023] [Indexed: 10/29/2023] Open
Abstract
Lung cancer is a highly aggressive neoplasm and, despite the development of recent therapies, tumor progression and recurrence following the initial response remains unsolved. Several questions remain unanswered about non-small cell lung cancer (NSCLC): (1) Which patients will actually benefit from therapy? (2) What are the predictive factors of response to MAbs and TKIs? (3) What are the best combination strategies with conventional treatments or new antineoplastic drugs? To answer these questions, an integrative literature review was carried out, searching articles in PUBMED, NCBI-PMC, Google Academic, and others. Here, we will examine the molecular genetics of lung cancer, emphasizing NSCLC, and delineate the primary categories of inhibitors based on their molecular targets, alongside the main treatment alternatives depending on the type of acquired resistance. We highlighted new therapies based on epigenetic information and a single-cell approach as a potential source of new biomarkers. The current and future of NSCLC management hinges upon genotyping correct prognostic markers, as well as on the evolution of precision medicine, which guarantees a tailored drug combination with precise targeting.
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Affiliation(s)
- Débora Dummer Meira
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Maria Clara de Castro e Caetano
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Matheus Correia Casotti
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Aléxia Stefani Siqueira Zetum
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - André Felipe Monteiro Gonçalves
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - André Rodrigues Moreira
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Augusto Henrique de Oliveira
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Fellipe Pesente
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Gabriel Mendonça Santana
- Centro de Ciências da Saúde, Curso de Medicina, Universidade Federal do Espírito Santo (UFES), Vitória 29090-040, Brazil
| | - Daniel de Almeida Duque
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Gierleson Santos Cangussu Pereira
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Giulia de Souza Cupertino de Castro
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Isabele Pagani Pavan
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - João Pedro Sarcinelli Chagas
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - José Henrique Borges Bourguignon
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Juliana Ribeiro de Oliveira
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Karen Ruth Michio Barbosa
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Lorena Souza Castro Altoé
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Luana Santos Louro
- Centro de Ciências da Saúde, Curso de Medicina, Universidade Federal do Espírito Santo (UFES), Vitória 29090-040, Brazil
| | - Luiza Poppe Merigueti
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Lyvia Neves Rebello Alves
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Marlon Ramos Rosado Machado
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Maria Luísa Rodrigues Oliveira Roque
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Pedro Santana Prates
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Sayuri Honorio de Paula Segáua
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Taissa dos Santos Uchiya
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Thomas Erik Santos Louro
- Escola Superior de Ciências da Santa Casa de Misericórdia de Vitória (EMESCAM), Curso de Medicina, Vitória 29027-502, Brazil
| | - Vinicius Eduardo Daleprane
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Yasmin Moreto Guaitolini
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Creuza Rachel Vicente
- Departamento de Medicina Social, Universidade Federal do Espírito Santo, Vitória 29090-040, Brazil
| | - Raquel Silva dos Reis Trabach
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Bruno Cancian de Araújo
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Eldamária de Vargas Wolfgramm dos Santos
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Flávia de Paula
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
| | - Tiago José S. Lopes
- Department of Reproductive Biology, National Center for Child Health and Development Research Institute, Tokyo 157-8535, Japan
| | - Elizeu Fagundes de Carvalho
- Instituto de Biologia Roberto Alcântara Gomes (IBRAG), Universidade do Estado do Rio de Janeiro (UERJ), Rio de Janeiro 20551-030, Brazil
| | - Iúri Drumond Louro
- Núcleo de Genética Humana e Molecular, Centro de Ciências Humanas e Naturais, Departamento de Ciências Biológicas, Universidade Federal do Espírito Santo (UFES), Vitória 29075-910, Brazil (M.C.C.)
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Wu R, Teng X, Song Q, Chen S, Wang L, Liao J, Zou C. Single-cell RNA sequencing reveals sexual diversity in the human bladder and its prospective impacts on bladder cancer and urinary tract infection. BMC Med Genomics 2023; 16:122. [PMID: 37277784 DOI: 10.1186/s12920-023-01535-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 05/09/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Some bladder-related diseases, such as bladder urinary tract infection (UTI) and bladder cancer (BCa), have significant six differences in incidence and prognosis. However, the molecular mechanisms underlying these sex differences are still not fully understood. Understanding the sex-biased differences in gene expression in normal bladder cells can help resolve these problems. METHODS We first collected published single-cell RNA sequencing (scRNA-seq) data of normal human bladders from females and males to map the bladder transcriptomic landscape. Then, Gene Ontology (GO) analysis and gene set enrichment analysis (GSEA) were used to determine the significant pathways that changed in the specific cell populations. The Monocle2 package was performed to reconstruct the differentiation trajectories of fibroblasts. In addition, the scMetabolism package was used to analyze the metabolic activity at the single-cell level, and the SCENIC package was used to analyze the regulatory network. RESULTS In total, 27,437 cells passed stringent quality control, and eight main cell types in human bladder were identified according to classical markers. Sex-based differential gene expression profiles were mainly observed in human bladder urothelial cells, fibroblasts, B cells, and T cells. We found that urothelial cells in males demonstrated a higher growth rate. Moreover, female fibroblasts produced more extracellular matrix, including seven collagen genes that may mediate BCa progression. Furthermore, the results showed that B cells in female bladders exhibited more B-cell activated signals and a higher expression of immunoglobulin genes. We also found that T cells in female bladders exhibited more T-cell activated signals. These different biological functions and properties of these cell populations may correlate with sex differences in UTI and BCa, and result in different disease processes and outcomes. CONCLUSIONS Our study provides reasonable insights for further studies of sex-based physiological and pathological disparities in the human bladder, which will contribute to the understanding of epidemiological differences in UTI and BCa.
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Affiliation(s)
- Ribao Wu
- Center for Translational Medicine, Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Institute of Neuroscience and Guangxi Key Laboratory of Brain Science, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China
| | - Xiahong Teng
- School of International Education, Guangxi Medical University, Nanning, Guangxi, China
| | - Qiong Song
- Center for Translational Medicine, Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Institute of Neuroscience and Guangxi Key Laboratory of Brain Science, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China
| | - Shuai Chen
- Center for Translational Medicine, Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Institute of Neuroscience and Guangxi Key Laboratory of Brain Science, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China
| | - Lihui Wang
- Center for Translational Medicine, Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Institute of Neuroscience and Guangxi Key Laboratory of Brain Science, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China
| | - Jinling Liao
- Center for Genomic and Personalized Medicine, Guangxi Medical University, Nanning, Guangxi, China
| | - Chunlin Zou
- Center for Translational Medicine, Key Laboratory of Longevity and Aging-related Diseases of Chinese Ministry of Education, Institute of Neuroscience and Guangxi Key Laboratory of Brain Science, School of Basic Medical Sciences, Guangxi Medical University, Nanning, Guangxi, China.
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