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Ding Y, Ye Z, Ding B, Feng S, Zhang Y, Shen Y. Identification of CXCL13 as a Promising Biomarker for Immune Checkpoint Blockade Therapy and PARP Inhibitor Therapy in Ovarian Cancer. Mol Biotechnol 2024:10.1007/s12033-024-01207-5. [PMID: 38856873 DOI: 10.1007/s12033-024-01207-5] [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: 02/13/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024]
Abstract
Ovarian cancer has poor response rates to immune checkpoint blockade (ICB) therapy, despite the use of genomic sequencing to identify molecular targets. Homologous recombination deficiency (HRD) is a conventional indicator of genomic instability (GI) and has been used as a marker for targeted therapies. Indicators reflecting HRD status have shown potential in predicting the efficacy of ICB treatment. Public databases, including TCGA, ICGC, and GEO, were used to obtain data. HRD scores, neoantigen load, and TMB were obtained from the TCGA cohort. Candidate biomarkers were validated in multiple databases, such as the Imvigor210 immunotherapy cohort and the open-source single-cell sequencing database. Immunohistochemistry was performed to further validate the results in independent cohorts. CXCL10, CXCL11, and CXCL13 were found to be significantly upregulated in HRD tumors and exhibited prognostic value. A comprehensive analysis of the tumor immune microenvironment (TIME) revealed that CXCL13 expression positively correlated with neoantigen load and immune cell infiltration. In addition, single-cell sequencing data and clinical trial results supported the utility of CXCL13 as a biomarker for ICB therapy. Not only does CXCL13 serve as a biomarker reflecting HRD status, but it also introduces a potentially novel perspective on prognostic biomarkers for ICB in ovarian cancer.
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Affiliation(s)
- Yue Ding
- Department of Obstetrics and Gynaecology, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Zheng Ye
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, 210096, China
| | - Bo Ding
- Department of Obstetrics and Gynaecology, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Songwei Feng
- Department of Obstetrics and Gynaecology, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China
| | - Yang Zhang
- Department of Obstetrics and Gynecology, First People's Hospital of Lianyungang, No. 6 East Zhenhua Road, Haizhou, Lianyungang, China.
| | - Yang Shen
- Department of Obstetrics and Gynaecology, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, China.
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2
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Kasperski A, Heng HH. The Digital World of Cytogenetic and Cytogenomic Web Resources. Methods Mol Biol 2024; 2825:361-391. [PMID: 38913321 DOI: 10.1007/978-1-0716-3946-7_21] [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: 06/25/2024]
Abstract
The dynamic growth of technological capabilities at the cellular and molecular level has led to a rapid increase in the amount of data on the genes and genomes of organisms. In order to store, access, compare, validate, classify, and understand the massive data generated by different researchers, and to promote effective communication among research communities, various genome and cytogenetic online databases have been established. These data platforms/resources are essential not only for computational analyses and theoretical syntheses but also for helping researchers select future research topics and prioritize molecular targets. Furthermore, they are valuable for identifying shared recurrent genomic patterns related to human diseases and for avoiding unnecessary duplications among different researchers. The website interface, menu, graphics, animations, text layout, and data from databases are displayed by a front end on the screen of a monitor or smartphone. A database front-end refers to the user interface or application that enables accessing tabular, structured, or raw data stored in the database. The Internet makes it possible to reach a greater number of users around the world and gives them quick access to information stored in databases. The number of ways of presenting this data by front-ends increases as well. This requires unifying the ways of operating and presenting information by front-ends and ensuring contextual switching between front-ends of different databases. This chapter aims to present selected cytogenetic and cytogenomic Internet resources in terms of obtaining the needed information and to indicate how to increase the efficiency of access to stored information. Through a brief introduction of these databases and by providing examples of their usage in cytogenetic analyses, we aim to bridge the gap between cytogenetics and molecular genomics by encouraging their utilization.
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Affiliation(s)
- Andrzej Kasperski
- Institute of Biological Sciences, Department of Biotechnology, Laboratory of Bioinformatics and Control of Bioprocesses, University of Zielona Góra, Zielona Góra, Poland.
| | - Henry H Heng
- Center for Molecular Medicine and Genetics, and Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA
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Zhang X, Kschischo M. Profiling Numerical and Structural Chromosomal Instability in Different Cancer Types. Methods Mol Biol 2024; 2825:345-360. [PMID: 38913320 DOI: 10.1007/978-1-0716-3946-7_20] [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: 06/25/2024]
Abstract
Many cancers display whole chromosome instability (W-CIN) and structural chromosomal instability (S-CIN), referring to increased rates of acquiring numerically and structurally abnormal chromosome changes. This protocol provides detailed steps to analyze the W-CIN and S-CIN across cancer types, intending to leverage large-scale bulk sequencing and SNP array data complemented with the computational models to gain a better understanding of W-CIN and S-CIN.
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Affiliation(s)
- Xiaoxiao Zhang
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, Remagen, Germany
- Department of Informatics, Technical University of Munich, Munich, Germany
| | - Maik Kschischo
- Department of Mathematics and Technology, University of Applied Sciences Koblenz, Remagen, Germany.
- Institute for Computer Science, University of Koblenz, Koblenz, Germany.
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Ye JC, Heng HH. The New Era of Cancer Cytogenetics and Cytogenomics. Methods Mol Biol 2024; 2825:3-37. [PMID: 38913301 DOI: 10.1007/978-1-0716-3946-7_1] [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: 06/25/2024]
Abstract
The promises of the cancer genome sequencing project, combined with various -omics technologies, have raised questions about the importance of cancer cytogenetic analyses. It is suggested that DNA sequencing provides high resolution, speed, and automation, potentially replacing cytogenetic testing. We disagree with this reductionist prediction. On the contrary, various sequencing projects have unexpectedly challenged gene theory and highlighted the importance of the genome or karyotype in organizing gene network interactions. Consequently, profiling the karyotype can be more meaningful than solely profiling gene mutations, especially in cancer where karyotype alterations mediate cellular macroevolution dominance. In this chapter, recent studies that illustrate the ultimate importance of karyotype in cancer genomics and evolution are briefly reviewed. In particular, the long-ignored non-clonal chromosome aberrations or NCCAs are linked to genome or chromosome instability, genome chaos is linked to genome reorganization under cellular crisis, and the two-phased cancer evolution reconciles the relationship between genome alteration-mediated punctuated macroevolution and gene mutation-mediated stepwise microevolution. By further synthesizing, the concept of karyotype coding is discussed in the context of information management. Altogether, we call for a new era of cancer cytogenetics and cytogenomics, where an array of technical frontiers can be explored further, which is crucial for both basic research and clinical implications in the cancer field.
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Affiliation(s)
- Jing Christine Ye
- Department of Lymphoma/Myeloma, Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Henry H Heng
- Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA.
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Heng E, Thanedar S, Heng HH. Challenges and Opportunities for Clinical Cytogenetics in the 21st Century. Genes (Basel) 2023; 14:493. [PMID: 36833419 PMCID: PMC9956237 DOI: 10.3390/genes14020493] [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: 01/28/2023] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
The powerful utilities of current DNA sequencing technology question the value of developing clinical cytogenetics any further. By briefly reviewing the historical and current challenges of cytogenetics, the new conceptual and technological platform of the 21st century clinical cytogenetics is presented. Particularly, the genome architecture theory (GAT) has been used as a new framework to emphasize the importance of clinical cytogenetics in the genomic era, as karyotype dynamics play a central role in information-based genomics and genome-based macroevolution. Furthermore, many diseases can be linked to elevated levels of genomic variations within a given environment. With karyotype coding in mind, new opportunities for clinical cytogenetics are discussed to integrate genomics back into cytogenetics, as karyotypic context represents a new type of genomic information that organizes gene interactions. The proposed research frontiers include: 1. focusing on karyotypic heterogeneity (e.g., classifying non-clonal chromosome aberrations (NCCAs), studying mosaicism, heteromorphism, and nuclear architecture alteration-mediated diseases), 2. monitoring the process of somatic evolution by characterizing genome instability and illustrating the relationship between stress, karyotype dynamics, and diseases, and 3. developing methods to integrate genomic data and cytogenomics. We hope that these perspectives can trigger further discussion beyond traditional chromosomal analyses. Future clinical cytogenetics should profile chromosome instability-mediated somatic evolution, as well as the degree of non-clonal chromosomal aberrations that monitor the genomic system's stress response. Using this platform, many common and complex disease conditions, including the aging process, can be effectively and tangibly monitored for health benefits.
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Affiliation(s)
- Eric Heng
- Stanford University, 450 Jane Stanford Way, Stanford, CA 94305, USA
| | - Sanjana Thanedar
- Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Henry H. Heng
- Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI 48201, USA
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48201, USA
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Prime SS, Cirillo N, Parkinson EK. Escape from Cellular Senescence Is Associated with Chromosomal Instability in Oral Pre-Malignancy. BIOLOGY 2023; 12:biology12010103. [PMID: 36671795 PMCID: PMC9855962 DOI: 10.3390/biology12010103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 01/05/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023]
Abstract
An escape from cellular senescence through the development of unlimited growth potential is one of the hallmarks of cancer, which is thought to be an early event in carcinogenesis. In this review, we propose that the molecular effectors of senescence, particularly the inactivation of TP53 and CDKN2A, together with telomere attrition and telomerase activation, all lead to aneuploidy in the keratinocytes from oral potentially malignant disorders (OPMD). Premalignant keratinocytes, therefore, not only become immortal but also develop genotypic and phenotypic cellular diversity. As a result of these changes, certain clonal cell populations likely gain the capacity to invade the underlying connective tissue. We review the clinical implications of these changes and highlight a new PCR-based assay to identify aneuploid cell in fluids such as saliva, a technique that is extremely sensitive and could facilitate the regular monitoring of OPMD without the need for surgical biopsies and may avoid potential biopsy sampling errors. We also draw attention to recent studies designed to eliminate aneuploid tumour cell populations that, potentially, is a new therapeutic approach to prevent malignant transformations in OPMD.
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Affiliation(s)
- Stephen S. Prime
- Centre for Immunology and Regenerative Medicine, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
- Correspondence: (S.S.P.); (E.K.P.)
| | - Nicola Cirillo
- Melbourne Dental School, University of Melbourne, 720 Swanson Street, Melbourne, VIC 3053, Australia
| | - E. Kenneth Parkinson
- Centre for Immunology and Regenerative Medicine, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London E1 4NS, UK
- Correspondence: (S.S.P.); (E.K.P.)
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Kong S, Li R, Tian Y, Zhang Y, Lu Y, Ou Q, Gao P, Li K, Zhang Y. Single-cell omics: A new direction for functional genetic research in human diseases and animal models. Front Genet 2023; 13:1100016. [PMID: 36685871 PMCID: PMC9846559 DOI: 10.3389/fgene.2022.1100016] [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: 11/16/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Over the past decade, with the development of high-throughput single-cell sequencing technology, single-cell omics has been emerged as a powerful tool to understand the molecular basis of cellular mechanisms and refine our knowledge of diverse cell states. They can reveal the heterogeneity at different genetic layers and elucidate their associations by multiple omics analysis, providing a more comprehensive genetic map of biological regulatory networks. In the post-GWAS era, the molecular biological mechanisms influencing human diseases will be further elucidated by single-cell omics. This review mainly summarizes the development and trend of single-cell omics. This involves single-cell omics technologies, single-cell multi-omics technologies, multiple omics data integration methods, applications in various human organs and diseases, classic laboratory cell lines, and animal disease models. The review will reveal some perspectives for elucidating human diseases and constructing animal models.
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Affiliation(s)
- Siyuan Kong
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China,*Correspondence: Siyuan Kong, ; Yubo Zhang,
| | - Rongrong Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yunhan Tian
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China
| | - Yaqiu Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yuhui Lu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Qiaoer Ou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Peiwen Gao
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yubo Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, China,Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Animal Functional Genomics Group, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China,College of Life Science and Engineering, Foshan University, Foshan, China,*Correspondence: Siyuan Kong, ; Yubo Zhang,
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Liao YY, Cao WM. The progress in our understanding of CIN in breast cancer research. Front Oncol 2023; 13:1067735. [PMID: 36874134 PMCID: PMC9978327 DOI: 10.3389/fonc.2023.1067735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 01/02/2023] [Indexed: 02/18/2023] Open
Abstract
Chromosomal instability (CIN) is an important marker of cancer, which is closely related to tumorigenesis, disease progression, treatment efficacy, and patient prognosis. However, due to the limitations of the currently available detection methods, its exact clinical significance remains unknown. Previous studies have demonstrated that 89% of invasive breast cancer cases possess CIN, suggesting that it has potential application in breast cancer diagnosis and treatment. In this review, we describe the two main types of CIN and discuss the associated detection methods. Subsequently, we highlight the impact of CIN in breast cancer development and progression and describe how it can influence treatment and prognosis. The goal of this review is to provide a reference on its mechanism for researchers and clinicians.
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Affiliation(s)
- Yu-Yang Liao
- Wenzhou Medical University, Wenzhou, China.,Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
| | - Wen-Ming Cao
- Department of Breast Medical Oncology, Zhejiang Cancer Hospital, Hangzhou, China
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Böhly N, Schmidt AK, Zhang X, Slusarenko BO, Hennecke M, Kschischo M, Bastians H. Increased replication origin firing links replication stress to whole chromosomal instability in human cancer. Cell Rep 2022; 41:111836. [PMID: 36516748 DOI: 10.1016/j.celrep.2022.111836] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 09/12/2022] [Accepted: 11/22/2022] [Indexed: 12/14/2022] Open
Abstract
Chromosomal instability (CIN) is a hallmark of cancer and comprises structural CIN (S-CIN) and numerical or whole chromosomal CIN (W-CIN). Recent work indicated that replication stress (RS), known to contribute to S-CIN, also affects mitotic chromosome segregation, possibly explaining the common co-existence of S-CIN and W-CIN in human cancer. Here, we show that RS-induced increased origin firing is sufficient to trigger W-CIN in human cancer cells. We discovered that overexpression of origin firing genes, including GINS1 and CDC45, correlates with W-CIN in human cancer specimens and causes W-CIN in otherwise chromosomally stable human cells. Furthermore, modulation of the ATR-CDK1-RIF1 axis increases the number of firing origins and leads to W-CIN. Importantly, chromosome missegregation upon additional origin firing is mediated by increased mitotic microtubule growth rates, a mitotic defect prevalent in chromosomally unstable cancer cells. Thus, our study identifies increased replication origin firing as a cancer-relevant trigger for chromosomal instability.
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Affiliation(s)
- Nicolas Böhly
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Ann-Kathrin Schmidt
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Xiaoxiao Zhang
- University of Applied Sciences Koblenz, Department of Mathematics and Technology, 53424 Remagen, Germany; Technical University of Munich, Department of Informatics, 81675 Munich, Germany
| | - Benjamin O Slusarenko
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Magdalena Hennecke
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany
| | - Maik Kschischo
- University of Applied Sciences Koblenz, Department of Mathematics and Technology, 53424 Remagen, Germany
| | - Holger Bastians
- Georg August University Göttingen, University Medical Center Göttingen (UMG), Department of Molecular Oncology, Section for Cellular Oncology, 37077 Göttingen, Germany.
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