101
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Qiao Y, Huang X, Moos PJ, Ahmann JM, Pomicter AD, Deininger MW, Byrd JC, Woyach JA, Stephens DM, Marth GT. A Bayesian framework to study tumor subclone-specific expression by combining bulk DNA and single-cell RNA sequencing data. Genome Res 2024; 34:94-105. [PMID: 38195207 PMCID: PMC10903947 DOI: 10.1101/gr.278234.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 11/22/2023] [Indexed: 01/11/2024]
Abstract
Genetic and gene expression heterogeneity is an essential hallmark of many tumors, allowing the cancer to evolve and to develop resistance to treatment. Currently, the most commonly used data types for studying such heterogeneity are bulk tumor/normal whole-genome or whole-exome sequencing (WGS, WES); and single-cell RNA sequencing (scRNA-seq), respectively. However, tools are currently lacking to link genomic tumor subclonality with transcriptomic heterogeneity by integrating genomic and single-cell transcriptomic data collected from the same tumor. To address this gap, we developed scBayes, a Bayesian probabilistic framework that uses tumor subclonal structure inferred from bulk DNA sequencing data to determine the subclonal identity of cells from single-cell gene expression (scRNA-seq) measurements. Grouping together cells representing the same genetically defined tumor subclones allows comparison of gene expression across different subclones, or investigation of gene expression changes within the same subclone across time (i.e., progression, treatment response, or relapse) or space (i.e., at multiple metastatic sites and organs). We used simulated data sets, in silico synthetic data sets, as well as biological data sets generated from cancer samples to extensively characterize and validate the performance of our method, as well as to show improvements over existing methods. We show the validity and utility of our approach by applying it to published data sets and recapitulating the findings, as well as arriving at novel insights into cancer subclonal expression behavior in our own data sets. We further show that our method is applicable to a wide range of single-cell sequencing technologies including single-cell DNA sequencing as well as Smart-seq and 10x Genomics scRNA-seq protocols.
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Affiliation(s)
- Yi Qiao
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Xiaomeng Huang
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA
| | - Philip J Moos
- Department of Pharmacology and Toxicology, University of Utah, Salt Lake City, Utah 84112, USA
| | - Jonathan M Ahmann
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Anthony D Pomicter
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Michael W Deininger
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
- Division of Hematology and Hematologic Malignancies, University of Utah, Salt Lake City, Utah 84112, USA
| | - John C Byrd
- The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Jennifer A Woyach
- The James Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, USA
| | - Deborah M Stephens
- Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA
| | - Gabor T Marth
- Eccles Institute of Human Genetics, University of Utah, Salt Lake City, Utah 84112, USA;
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102
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Salu P, Reindl KM. Advancements in Preclinical Models of Pancreatic Cancer. Pancreas 2024; 53:e205-e220. [PMID: 38206758 PMCID: PMC10842038 DOI: 10.1097/mpa.0000000000002277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2024]
Abstract
ABSTRACT Pancreatic cancer remains one of the deadliest of all cancer types with a 5-year overall survival rate of just 12%. Preclinical models available for understanding the disease pathophysiology have evolved significantly in recent years. Traditionally, commercially available 2-dimensional cell lines were developed to investigate mechanisms underlying tumorigenesis, metastasis, and drug resistance. However, these cells grow as monolayer cultures that lack heterogeneity and do not effectively represent tumor biology. Developing patient-derived xenografts and genetically engineered mouse models led to increased cellular heterogeneity, molecular diversity, and tissues that histologically represent the original patient tumors. However, these models are relatively expensive and very timing consuming. More recently, the advancement of fast and inexpensive in vitro models that better mimic disease conditions in vivo are on the rise. Three-dimensional cultures like organoids and spheroids have gained popularity and are considered to recapitulate complex disease characteristics. In addition, computational genomics, transcriptomics, and metabolomic models are being developed to simulate pancreatic cancer progression and predict better treatment strategies. Herein, we review the challenges associated with pancreatic cancer research and available analytical models. We suggest that an integrated approach toward using these models may allow for developing new strategies for pancreatic cancer precision medicine.
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Affiliation(s)
- Philip Salu
- From the Department of Biological Sciences, North Dakota State University, Fargo, ND
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103
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Zhu Q, Dai H, Qiu F, Lou W, Wang X, Deng L, Shi C. Heterogeneity of computational pathomic signature predicts drug resistance and intra-tumor heterogeneity of ovarian cancer. Transl Oncol 2024; 40:101855. [PMID: 38185058 PMCID: PMC10808968 DOI: 10.1016/j.tranon.2023.101855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 01/09/2024] Open
Abstract
BACKGROUND Chemotherapy resistance is the main cause of ovarian cancer progression and even death. However, there are no clear indicators for predicting the risk of drug resistance in patients. Intra-tumor heterogeneity (ITH) is one of the characteristics of malignant tumors, which is associated with the treatment and prognosis of tumors. Accordingly, our study aims to investigate the correlation between the image features of intra-tumor heterogeneity and drug resistance of ovarian cancer based on artificial intelligence. METHODS We obtained hematoxylin and eosin staining frozen histopathological images of ovarian cancer and paracarcinoma tissues from the Cancer Genome Atlas. We extracted quantitative image features of whole-slide images based on the automatic image nuclear segmentation processing technology. After that, we used bioinformatics analysis to find the relationship between image features of intra-tumor heterogeneity and drug resistance. RESULTS Our results show that our automatic image processing process based on computer artificial intelligence can extract image features effectively, and the key image features extracted are closely related to ITH. Among them, the Perimeter.sd image feature with the most prominent ITH feature can accurately predict the risk of platinum-based chemotherapy drug resistance in ovarian cancer patients. CONCLUSION Automatic image processing and feature extraction based on artificial intelligence have excellent results. Perimeter.sd can be used as a useful image feature indicator for evaluating ITH. ITH is associated with drug resistance of ovarian cancer, so ITH characteristics can be used as an effective indicator to evaluate drug resistance in patients with ovarian cancer.
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Affiliation(s)
- Qiuli Zhu
- Department of Genetics, Gaoxin Branch of The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hua Dai
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Feng Qiu
- Department of Oncology, Gaoxin Branch of The First Affiliated Hospital of Nanchang University, No.7889 of Changdong avenue, Gaoxin District, Nanchang, Jiangxi, China
| | - Weiming Lou
- The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xin Wang
- Queen Mary School of Nanchang University, Nanchang University, Nanchang, China
| | - Libin Deng
- Jiangxi Provincial Key Laboratory of Preventive Medicine, School of Public Health, Nanchang University, Nanchang, China.
| | - Chao Shi
- Department of Oncology, Gaoxin Branch of The First Affiliated Hospital of Nanchang University, No.7889 of Changdong avenue, Gaoxin District, Nanchang, Jiangxi, China.
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104
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Li J, Li S, Shu M, Hu W. Unravelling the heterogeneity of oral squamous cell carcinoma by integrative analysis of single-cell and bulk transcriptome data. J Cell Mol Med 2024; 28:e18108. [PMID: 38279519 PMCID: PMC10844683 DOI: 10.1111/jcmm.18108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 01/28/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) is a prevalent malignancy of the head and neck with rising global incidence. Despite advances in treatment modalities, OSCC prognosis remains diverse due to the complex molecular and cellular heterogeneity within tumours, as well as the heterogeneity in tumour microenvironment (TME). In this study, we utilized single-cell RNA sequencing (scRNA-seq) analysis to explore distinct subpopulations of tumour cells in OSCC tissues and their interaction with components in TME. We identified four major tumour cell subpopulations (C0, C1, C2 and C3) with unique molecular characteristics and functional features. Pathway enrichment analysis revealed that C0 primarily expressed genes involved in extracellular matrix interactions and C1 showed higher proliferation levels, suggesting that the two cell subpopulations exhibited tumour aggressiveness. Conversely, C2 and C3 displayed features associated with keratinization and cornified envelope formation. Accordingly, C0 and C1 subpopulations were associated with shorter overall and disease-free survival times, while C2 and C3 were weakly correlated with longer survival. Genomic analysis showed that C1 demonstrated a positive correlation with tumour mutation burden. Furthermore, C0 exhibited resistant to cisplatin treatment, while C1 showed more sensitive to cisplatin treatment, indicating that C0 might exhibit more aggressive compared to C1. Additionally, C0 had a higher level of communication with fibroblasts and endothelial cells in TME via integrin-MAPK signalling, suggesting that the function of C0 was maintained by that pathway. In summary, this study provided critical insights into the molecular and cellular heterogeneity of OSCC, with potential implications for prognosis prediction and personalized therapeutic approaches.
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Affiliation(s)
- Jia Li
- Department of ProsthodonticsShanghai Engineering Research Center of Tooth Restoration and RegenerationStomatological Hospital and Dental School of Tongji UniversityShanghaiChina
| | - Shengjiao Li
- Department of Oral and Maxillofacial SurgeryShanghai Engineering Research Center of Tooth Restoration and RegenerationStomatological Hospital and Dental School of Tongji UniversityShanghaiChina
| | - Mingyang Shu
- Department of StomatologyHuai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical UniversityHuai'anChina
| | - Weiwei Hu
- Department of StomatologyHuai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical UniversityHuai'anChina
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105
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Liu H, Zheng Q, Li M, Kou J, Wei J, Feng W. Dose-dependent bidirectional pharmacological effects of vinorelbine-based metronomic combination chemotherapy on tumor growth and metastasis and mechanisms in melanoma mouse model. Fundam Clin Pharmacol 2024; 38:99-112. [PMID: 37458143 DOI: 10.1111/fcp.12939] [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: 02/07/2023] [Revised: 03/25/2023] [Accepted: 06/26/2023] [Indexed: 07/18/2023]
Abstract
BACKGROUND There is evidence that the empirical setting of doses and schedules of antineoplastic agents in metronomic chemotherapy (MC) might lead to undesirable outcomes, such as promoting tumor growth or metastasis at certain low doses. However, details about the dose effect of antineoplastic agents in MC have not been fully known yet. OBJECTIVES Vinorelbine combined with cisplatin or fluorouracil (VNR/CDDP or VNR/FU) was selected to investigate its effects on tumor growth or metastasis as well as mechanisms. METHODS Experimental techniques, including immunohistochemistry, western blot, immunofluorescence, and flow cytometry, were used to explore the mechanisms, along with cell proliferation, apoptosis, migration, and invasion. RESULTS The results showed that VNR/CDDP or VNR/FU promoted tumor growth and metastasis at low doses and inhibited them at high ones. Except that expressions of apoptotic proteins were elevated at both low and high doses, low-dose treatments enhanced angiogenesis and promoted the mobilization and recruitment of myeloid-derived suppressor cells (MDSCs), while high-dose treatments reversed these effects. Additionally, low concentrations of VNR/CDDP or VNR/FU stimulated tumor cell functions such as anti-apoptosis, migration, and invasion, but high concentrations only suppressed cell proliferation and increased apoptosis. CONCLUSION This study elucidated a bidirectional action mode regulated by multiple mechanisms at different doses in MC and also highlighted the risks of low-dose metronomic administration of antineoplastic agents in the clinic. More preclinical and clinical studies focusing on the dose-effect of metronomic regimens are urgently needed because an effective therapeutic regimen should be an optimal setting of drugs, doses, schedules, or combinations.
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Affiliation(s)
- Hua Liu
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Qiaowei Zheng
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Min Li
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Jianrong Kou
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Junsong Wei
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
| | - Weiyi Feng
- Department of Pharmacy, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, PR China
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106
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Xue W, Wang T, Tian WJ, Pang SQ, Zhang HF, Jia WD. NQO1 Mediates Lenvatinib Resistance by Regulating ROS-induced Apoptosis in Hepatocellular Carcinoma. Curr Med Sci 2024; 44:168-179. [PMID: 38217831 DOI: 10.1007/s11596-023-2804-8] [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: 05/30/2023] [Accepted: 09/19/2023] [Indexed: 01/15/2024]
Abstract
OBJECTIVE Hepatocellular carcinoma (HCC) is the third leading cause of cancer-associated death worldwide. As a first-line drug for advanced HCC treatment, lenvatinib faces a significant hurdle due to the development of both intrinsic and acquired resistance among patients, and the underlying mechanism remains largely unknown. The present study aims to identify the pivotal gene responsible for lenvatinib resistance in HCC, explore the potential molecular mechanism, and propose combinatorial therapeutic targets for HCC management. METHODS Cell viability and colony formation assays were conducted to evaluate the sensitivity of cells to lenvatinib and dicoumarol. RNA-Seq was used to determine the differences in transcriptome between parental cells and lenvatinib-resistant (LR) cells. The upregulated genes were analyzed by GO and KEGG analyses. Then, qPCR and Western blotting were employed to determine the relative gene expression levels. Afterwards, the intracellular reactive oxygen species (ROS) and apoptosis were detected by flow cytometry. RESULTS PLC-LR and Hep3B-LR were established. There was a total of 116 significantly upregulated genes common to both LR cell lines. The GO and KEGG analyses indicated that these genes were involved in oxidoreductase and dehydrogenase activities, and reactive oxygen species pathways. Notably, NAD(P)H:quinone oxidoreductase 1 (NQO1) was highly expressed in LR cells, and was involved in the lenvatinib resistance. The high expression of NQO1 decreased the production of ROS induced by lenvatinib, and subsequently suppressed the apoptosis. The combination of lenvatinib and NQO1 inhibitor, dicoumarol, reversed the resistance of LR cells. CONCLUSION The high NQO1 expression in HCC cells impedes the lenvatinib-induced apoptosis by regulating the ROS levels, thereby promoting lenvatinib resistance in HCC cells.
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Affiliation(s)
- Wei Xue
- Department of General Surgery, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, 230601, China
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Ting Wang
- Department of General Surgery, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Wen-Jing Tian
- Department of General Surgery, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Si-Qi Pang
- Department of General Surgery, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, 230601, China
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China
| | - Hua-Feng Zhang
- Department of General Surgery, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China.
- Institute of Health and Medicine, Hefei Comprehensive National Science Center, Hefei, 230601, China.
- The Chinese Academy of Sciences Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China.
| | - Wei-Dong Jia
- Department of General Surgery, The First Affiliated Hospital of University of Science and Technology of China, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, 230027, China.
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107
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Baker TM, Waise S, Tarabichi M, Van Loo P. Aneuploidy and complex genomic rearrangements in cancer evolution. NATURE CANCER 2024; 5:228-239. [PMID: 38286829 PMCID: PMC7616040 DOI: 10.1038/s43018-023-00711-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Accepted: 12/14/2023] [Indexed: 01/31/2024]
Abstract
Mutational processes that alter large genomic regions occur frequently in developing tumors. They range from simple copy number gains and losses to the shattering and reassembly of entire chromosomes. These catastrophic events, such as chromothripsis, chromoplexy and the formation of extrachromosomal DNA, affect the expression of many genes and therefore have a substantial effect on the fitness of the cells in which they arise. In this review, we cover large genomic alterations, the mechanisms that cause them and their effect on tumor development and evolution.
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Affiliation(s)
- Toby M Baker
- The Francis Crick Institute, London, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Sara Waise
- The Francis Crick Institute, London, UK
- Cancer Sciences Unit, University of Southampton, Southampton, UK
| | - Maxime Tarabichi
- The Francis Crick Institute, London, UK
- Institute for Interdisciplinary Research (IRIBHM), Université Libre de Bruxelles, Brussels, Belgium
| | - Peter Van Loo
- The Francis Crick Institute, London, UK.
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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108
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Pierik AS, Poell JB, Brink A, Stigter-van Walsum M, de Roest RH, Poli T, Yaromin A, Lambin P, Leemans CR, Brakenhoff RH. Intratumor genetic heterogeneity and head and neck cancer relapse. Radiother Oncol 2024; 191:110087. [PMID: 38185257 DOI: 10.1016/j.radonc.2024.110087] [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: 08/02/2023] [Revised: 12/18/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
BACKGROUND Head and neck squamous cell carcinomas are treated by surgery, radiotherapy (RT), chemoradiotherapy (CRT) or combinations thereof, but locoregional recurrences (LRs) occur in 30-40% of treated patients. We have previously shown that in approximately half of the LRs after CRT, cancer driver mutations are not shared with the index tumor. AIM To investigate two possible explanations for these genetically unrelated relapses, treatment-induced genetic changes and intratumor genetic heterogeneity. METHODS To investigate treatment-induced clonal DNA changes, we compared copy number alterations (CNAs) and mutations between primary and recurrent xenografted tumors after treatment with (C)RT. Intratumor genetic heterogeneity was studied by multi-region sequencing on DNA from 31 biopsies of 11 surgically treated tumors. RESULTS Induction of clonal DNA changes by (C)RT was not observed in the xenograft models. Multi-region sequencing demonstrated variations in CNA profiles between paired biopsies of individual tumors, with copy number heterogeneity scores varying from 0.027 to 0.333. In total, 32 cancer driver mutations could be identified and were shared in all biopsies of each tumor. Remarkably, multi-clonal mutations in these same cancer driver genes were observed in 6 of 11 tumors. Genetically distinct heterogeneous cell cultures could also be established from single tumors, with different biomarker profiles and drug sensitivities. CONCLUSION Intratumor genetic heterogeneity at the level of the cancer driver mutations might explain the discordant mutational profiles in LRs after CRT, while there are no indications in xenograft models that these changes are induced by CRT.
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Affiliation(s)
- A S Pierik
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Otolaryngology/Head and Neck Surgery, Head and Neck Cancer Biology and Immunology laboratory, De Boelelaan 1117, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
| | - J B Poell
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Otolaryngology/Head and Neck Surgery, Head and Neck Cancer Biology and Immunology laboratory, De Boelelaan 1117, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
| | - A Brink
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Otolaryngology/Head and Neck Surgery, Head and Neck Cancer Biology and Immunology laboratory, De Boelelaan 1117, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
| | - M Stigter-van Walsum
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Otolaryngology/Head and Neck Surgery, Head and Neck Cancer Biology and Immunology laboratory, De Boelelaan 1117, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
| | - R H de Roest
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Otolaryngology/Head and Neck Surgery, Head and Neck Cancer Biology and Immunology laboratory, De Boelelaan 1117, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands
| | - T Poli
- Maxillofacial Surgery Unit, Department of Medicine and Surgery - University of Parma, University Hospital of Parma, Via Gramsci 14, Parma, Italy
| | - A Yaromin
- Maastricht University, Department of Precision Medicine-UM & Radiology-MUMC, Universiteitssingel 40, Maastricht, the Netherlands
| | - P Lambin
- Maastricht University, Department of Precision Medicine-UM & Radiology-MUMC, Universiteitssingel 40, Maastricht, the Netherlands
| | - C R Leemans
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Otolaryngology/Head and Neck Surgery, Head and Neck Cancer Biology and Immunology laboratory, De Boelelaan 1117, Amsterdam, the Netherlands
| | - R H Brakenhoff
- Amsterdam UMC location Vrije Universiteit Amsterdam, Department of Otolaryngology/Head and Neck Surgery, Head and Neck Cancer Biology and Immunology laboratory, De Boelelaan 1117, Amsterdam, the Netherlands; Cancer Center Amsterdam, Cancer Biology and Immunology, De Boelelaan 1117, Amsterdam, the Netherlands.
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109
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Chen H, Song A, Ul Rehman F, Han D. Multidimensional progressive single-cell sequencing reveals cell microenvironment composition and cancer heterogeneity in lung cancer. ENVIRONMENTAL TOXICOLOGY 2024; 39:890-904. [PMID: 37956258 DOI: 10.1002/tox.24018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 10/11/2023] [Accepted: 10/18/2023] [Indexed: 11/15/2023]
Abstract
Despite substantial advances in cancer biology and treatment, the clinical outcomes of patients with lung cancer remain unsatisfactory. The tumor microenvironment (TME) is a potential target. Using single-cell RNA sequencing, we could distinguish eight distinct cell types in the lung cancer microenvironment, demonstrating substantial intratumoral heterogeneity in 19 different lung cancer tumor samples. Through the re-dimensional grouping of cancer-associated fibroblasts (CAFs), myeloid cells, epithelial cells, natural killer (NK) cells, and T cells, the difference in the TME of lung cancer was revealed. We discovered SFTPB, SFN, and KRT8 as possible predictive biomarkers for lung cancer by assessing the gene expression patterns in epithelial cells. Examining cell-to-cell communications showed a robust association between the quantity of matrix CAFs, epithelial cells, and macrophages in the thrombospondin signaling pathway. Additionally, we found that the amyloid precursor protein signaling pathway primarily originated from the matrix, and inflammatory cancer-associated endothelial and fibroblast cells showed a co-expression relationship with myeloid cells and B cells. Through cell-to-cell correlation analysis, we found positive regulation between NK cells, regulatory T cells, GZMB-CD8 T cells, and GZMK-CD8 T cells, which could play a role in developing immune TMEs. These findings support studies on cancer heterogeneity and add to our understanding of lung cancer's cellular microenvironment.
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Affiliation(s)
- Hua Chen
- Department of Research and Development, Qingdao Bioman Biomedical Technology Co., LTD, Qingdao, China
- Department of Research and Development, Shanghai life Biomedical Technology Co., LTD, Shanghai, China
| | - Anqi Song
- Department of Student Affairs, The 2nd Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Faisal Ul Rehman
- Precision Medicine Center of Oncology, The Affiliated Hospital of Qingdao University, Qingdao, China
| | - Dan Han
- Department of Emergency Medicine and Intensive Care, Shanghai Songjiang District Central Hospital, Shanghai, China
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110
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Hu X, Chi H, Fu X, Chen J, Dong L, Jiang S, Li Y, Chen J, Cheng M, Min Q, Tian Y, Zhang P. Tunable Multivalent Aptamer-Based DNA Nanostructures To Regulate Multiheteroreceptor-Mediated Tumor Recognition. J Am Chem Soc 2024; 146:2514-2523. [PMID: 38247135 DOI: 10.1021/jacs.3c10704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
Precise mapping and regulation of cell surface receptors hold immense significance in disease treatment, such as cancer, infection, and neurodisorders, but also face enormous challenges. In this study, we designed a series of adjustable multivalent aptamer-based DNA nanostructures to precisely control their interaction with receptors in tumor cells. By profiling surface receptors on 12 cell lines using 10 different aptamers, we generated a heatmap that accurately distinguished between various tumor types based on multiple markers. We then incorporated these aptamers onto DNA origami structures to regulate receptor recognition, with patch-like structures demonstrating a tendency to be trapped on the cell surface and with tube-like structures showing a preference for internalization. Through precise control of aptamer species, valence, and geometric patterns, we found that multiheteroreceptor-mediated recognition not only favored the specific binding of nanostructures to tumor cells but also greatly enhanced intracellular uptake by promoting clathrin-dependent endocytosis. Specifically, we achieved over 5-fold uptake in different tumor cells versus normal cells using tube-like structures modified with different diheteroaptamer pairs, facilitating targeted drug delivery. Moreover, patch-like structures with triheteroaptamers guided specific interactions between macrophages and tumor cells, leading to effective immune clearance. This programmable multivalent system allows for the precise regulation of cell recognition using multiple parameters, demonstrating great potential for personalized tumor treatment.
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Affiliation(s)
- Xiaoxue Hu
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China
| | - Hongli Chi
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Xiaoyi Fu
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jinling Chen
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Linying Dong
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Shiqi Jiang
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Yan Li
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Jingyi Chen
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Ming Cheng
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
| | - Qianhao Min
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China
| | - Ye Tian
- College of Engineering and Applied Sciences, State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center, Nanjing University, Nanjing 210023, China
| | - Penghui Zhang
- Zhejiang Cancer Hospital, The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou 310022, China
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111
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Antonello A, Bergamin R, Calonaci N, Househam J, Milite S, Williams MJ, Anselmi F, d'Onofrio A, Sundaram V, Sosinsky A, Cross WCH, Caravagna G. Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc. Genome Biol 2024; 25:38. [PMID: 38297376 PMCID: PMC10832148 DOI: 10.1186/s13059-024-03170-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 01/10/2024] [Indexed: 02/02/2024] Open
Abstract
Copy number alterations (CNAs) are among the most important genetic events in cancer, but their detection from sequencing data is challenging because of unknown sample purity, tumor ploidy, and general intra-tumor heterogeneity. Here, we present CNAqc, an evolution-inspired method to perform the computational validation of clonal and subclonal CNAs detected from bulk DNA sequencing. CNAqc is validated using single-cell data and simulations, is applied to over 4000 TCGA and PCAWG samples, and is incorporated into the validation process for the clinically accredited bioinformatics pipeline at Genomics England. CNAqc is designed to support automated quality control procedures for tumor somatic data validation.
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Affiliation(s)
- Alice Antonello
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Riccardo Bergamin
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Nicola Calonaci
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Jacob Househam
- Evolution and Cancer Lab, Centre for Genomics and Computational Biology, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Salvatore Milite
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
- Centre for Computational Biology, Human Technopole, Milan, Italy
| | - Marc J Williams
- Department of Computational Oncology, Memorial Sloan Kettering, New York, USA
| | - Fabio Anselmi
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | - Alberto d'Onofrio
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy
| | | | | | - William C H Cross
- Department of Research Pathology, UCL Cancer Institute, University College London, London, UK
| | - Giulio Caravagna
- Department of Mathematics, Informatics and Geosciences (MIGe), University of Trieste, Trieste, Italy.
- Evolutionary Genomics and Modelling Team, Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
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112
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Ma JW, Jiang X, Wang YM, Jiang JM, Miao L, Qi LL, Zhang JX, Wen X, Li JW, Li M, Zhang L. Dual-energy CT-based radiomics in predicting EGFR mutation status non-invasively in lung adenocarcinoma. Heliyon 2024; 10:e24372. [PMID: 38304841 PMCID: PMC10831617 DOI: 10.1016/j.heliyon.2024.e24372] [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: 06/26/2023] [Revised: 12/15/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Objectives Patients with epidermal growth factor receptor (EGFR) mutations in lung adenocarcinoma (LUAD) can benefit from individualized targeted therapy. This study aims to develop, compare, analyse prediction models based on dual-energy spectral computed tomography (DESCT) and CT-based radiomic features to non-invasively predict EGFR mutation status in LUAD. Materials and methods Patients with LUAD (n = 175), including 111 patients with and 64 patients without EGFR mutations, were enrolled in the current study. All patients were randomly divided into a training dataset (122 cases) and validation dataset (53 cases) at a ratio of 7:3. After extracting CT-based radiomic, DESCT and clinical features, we built seven prediction models and a nomogram of the best prediction. Receiver operating characteristic (ROC) curves and the mean area under the curve (AUC) values were used for comparisons among the models to obtain the best prediction model for predicting EGFR mutations. Results The best distinguishing ability is the combined model incorporating radiomic, DESCT and clinical features for predicting the EGFR mutation status with an AUC of 0.86 (95 % CI: 0.79-0.92) in the training group and an AUC value of 0.83 (95 % CI: 0.73, 0.96) in the validation group. Conclusions Our study provides a predictive nomogram non-invasively with a combination of CT-based radiomic, DESCT and clinical features, which can provide image-based biological information for targeted therapy of LUAD with EGFR mutations.
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Affiliation(s)
- Jing-Wen Ma
- Department of Diagnostic Radiology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
- Department of Radiology, State Key Laboratory of Cardiovascular Disease, National Clinical Research Center for Cardiovascular Diseases, Fuwai Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, #167 Bei-Li-Shi Street, Beijing 100037, China
| | - Xu Jiang
- Department of Diagnostic Radiology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Yan-Mei Wang
- GE Healthcare China, Pudong New Town, Shanghai, China
| | - Jiu-Ming Jiang
- Department of Diagnostic Radiology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lei Miao
- Department of Diagnostic Radiology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lin-Lin Qi
- Department of Diagnostic Radiology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jia-Xing Zhang
- Department of Diagnostic Radiology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xin Wen
- Department of Diagnostic Radiology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Jian-Wei Li
- Department of Diagnostic Radiology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Meng Li
- Department of Diagnostic Radiology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Li Zhang
- Department of Diagnostic Radiology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
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113
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Lu Y, Chu Q, Li Z, Wang M, Gatenby R, Zhang Q. Deep reinforcement learning identifies personalized intermittent androgen deprivation therapy for prostate cancer. Brief Bioinform 2024; 25:bbae071. [PMID: 38493345 PMCID: PMC11174533 DOI: 10.1093/bib/bbae071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 01/11/2024] [Accepted: 02/03/2024] [Indexed: 03/18/2024] Open
Abstract
The evolution of drug resistance leads to treatment failure and tumor progression. Intermittent androgen deprivation therapy (IADT) helps responsive cancer cells compete with resistant cancer cells in intratumoral competition. However, conventional IADT is population-based, ignoring the heterogeneity of patients and cancer. Additionally, existing IADT relies on pre-determined thresholds of prostate-specific antigen to pause and resume treatment, which is not optimized for individual patients. To address these challenges, we framed a data-driven method in two steps. First, we developed a time-varied, mixed-effect and generative Lotka-Volterra (tM-GLV) model to account for the heterogeneity of the evolution mechanism and the pharmacokinetics of two ADT drugs Cyproterone acetate and Leuprolide acetate for individual patients. Then, we proposed a reinforcement-learning-enabled individualized IADT framework, namely, I$^{2}$ADT, to learn the patient-specific tumor dynamics and derive the optimal drug administration policy. Experiments with clinical trial data demonstrated that the proposed I$^{2}$ADT can significantly prolong the time to progression of prostate cancer patients with reduced cumulative drug dosage. We further validated the efficacy of the proposed methods with a recent pilot clinical trial data. Moreover, the adaptability of I$^{2}$ADT makes it a promising tool for other cancers with the availability of clinical data, where treatment regimens might need to be individualized based on patient characteristics and disease dynamics. Our research elucidates the application of deep reinforcement learning to identify personalized adaptive cancer therapy.
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Affiliation(s)
- Yitao Lu
- School of Data Science, City University of Hong Kong, Hong Kong SAR, China
| | - Qian Chu
- Department of Thoracic Oncology, Tongji Hospital, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Zhen Li
- Department of Radiology, Tongji Hospital, Huazhong University of Science and Technology, 430030, Wuhan, China
| | - Mengdi Wang
- Department of Electrical and Computer Engineering and the Center for Statistics and Machine Learning, Princeton University, 08544, NJ, U.S.A
| | - Robert Gatenby
- Department of Integrated Mathematical Oncology and the Cancer Biology and Evolution Program, H. Lee Moffitt Cancer Center and Research Institute, 33612, FL, USA
| | - Qingpeng Zhang
- Musketeers Foundation Institute of Data Science and the Department of Pharmacology and Pharmacy, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
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114
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Hu Y, Sun H, Shi W, Chen C, Wu X, Jiang Y, Zhang G, Li N, Song J, Zhang H, Shen B, Zeng H, Zhang H. Immunogram defines four cancer-immunity cycle phenotypes with distinct clonal selection patterns across solid tumors. J Transl Med 2024; 22:69. [PMID: 38243238 PMCID: PMC10799518 DOI: 10.1186/s12967-023-04765-5] [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: 05/19/2023] [Accepted: 11/27/2023] [Indexed: 01/21/2024] Open
Abstract
BACKGROUND The cancer-immunity cycle (CI cycle) provides a theoretical framework to illustrate the process of the anticancer immune response. Recently, the update of the CI cycle theory emphasizes the importance of tumor's immunological phenotype. However, there is lack of immunological phenotype of pan-cancer based on CI cycle theory. METHODS Here, we applied a visualizing method termed 'cancer immunogram' to visualize the state of CI cycle of 8460 solid tumors from TCGA cohort. Unsupervised clustering of the cancer immunogram was performed using the nonnegative matrix factorization (NMF) analysis. We applied an evolutionary genomics approach (dN/dS ratio) to evaluate the clonal selection patterns of tumors with distinct immunogram subtypes. RESULTS We defined four major CI cycle patterns across 32 cancer types using a cancer immunogram approach. Immunogram-I was characterized by 'hot' and 'exhausted' features, indicating a favorable prognosis. Strikingly, immunogram-II, immunogram-III, and immunogram-IV represented distinct immunosuppressive patterns of 'cold' tumor. Immunogram-II was characterized by 'cold' and 'radical' features, which represented increased expression of immune inhibitor molecules and high levels of positive selection, indicating the worst prognosis. Immunogram-III was characterized by 'cold' and 'recognizable' features and upregulated expression of MHC I molecules. Immunogram-IV was characterized by 'cold' and 'inert' features, which represented overall immunosuppression, lower levels of immunoediting and positive selection, and accumulation of more tumor neoantigens. In particular, favorable overall survival was observed in metastatic urothelial cancer patients with immunogram-I and immunogram-IV after immune checkpoint inhibitor (ICI) therapy. Meanwhile, a higher response rate to ICI therapy was observed in metastatic gastric cancer patients with immunogram-I phenotype. CONCLUSIONS Our findings provide new insight into the interaction between immunity and cancer evolution, which may contribute to optimizing immunotherapy strategies.
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Affiliation(s)
- Ying Hu
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
- Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Huaibo Sun
- Beijing SinoMDgene Technology CO., LTD, Beijing, 100176, China
| | - Wei Shi
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Chen Chen
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
- Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Xueying Wu
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
- Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Yu Jiang
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
- Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Guoying Zhang
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
- Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Na Li
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
- Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China
| | - Jin Song
- Beijing Immupeutics Medicine Technology Limited, Beijing, 102609, China
| | - Hao Zhang
- Department of General Surgery, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Baiyong Shen
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
- State Key Laboratory of Oncogenes and Related Genes, National Research Center for Translational Medicine (Shanghai), Shanghai, 200025, China.
| | - Hui Zeng
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China.
- Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China.
| | - Henghui Zhang
- Biomedical Innovation Center, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China.
- Beijing Key Laboratory for Therapeutic Cancer Vaccines, Beijing Shijitan Hospital, Capital Medical University, Beijing, 100038, China.
- Beijing Engineering Research Center of Immunocellular therapy, Beijing, 102609, China.
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115
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Mitchell J, Milite S, Bartram J, Walker S, Volkova N, Yavorska O, Zarowiecki M, Chalker J, Thomas R, Vago L, Sosinsky A, Caravagna G. Clinical application of tumour-in-normal contamination assessment from whole genome sequencing. Nat Commun 2024; 15:323. [PMID: 38238294 PMCID: PMC10796348 DOI: 10.1038/s41467-023-44158-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Accepted: 12/01/2023] [Indexed: 01/22/2024] Open
Abstract
The unexpected contamination of normal samples with tumour cells reduces variant detection sensitivity, compromising downstream analyses in canonical tumour-normal analyses. Leveraging whole-genome sequencing data available at Genomics England, we develop a tool for normal sample contamination assessment, which we validate in silico and against minimal residual disease testing. From a systematic review of [Formula: see text] patients with haematological malignancies and sarcomas, we find contamination across a range of cancer clinical indications and DNA sources, with highest prevalence in saliva samples from acute myeloid leukaemia patients, and sorted CD3+ T-cells from myeloproliferative neoplasms. Further exploration reveals 108 hotspot mutations in genes associated with haematological cancers at risk of being subtracted by standard variant calling pipelines. Our work highlights the importance of contamination assessment for accurate somatic variants detection in research and clinical settings, especially with large-scale sequencing projects being utilised to deliver accurate data from which to make clinical decisions for patient care.
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Affiliation(s)
| | - Salvatore Milite
- Computational Biology Research Centre, Human Technopole, Milan, Italy
- Cancer Data Science Laboratory, Department of Mathematics, Informatics and Geosciences, University of Trieste, Trieste, Italy
| | - Jack Bartram
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | | | | | | | | | - Jane Chalker
- Specialist Integrated Haematological Malignancy Diagnostic Service - Acquired Genomics, Great Ormond Street Hospital for Children, London, UK
| | - Rebecca Thomas
- Department of Haematology, Great Ormond Street Hospital for Children, London, UK
| | - Luca Vago
- Research Unit of Immunogenetics, Leukemia Genomics and Immunobiology, IRCCS Hospital San Raffaele, Milan, Italy
| | | | - Giulio Caravagna
- Cancer Data Science Laboratory, Department of Mathematics, Informatics and Geosciences, University of Trieste, Trieste, Italy.
- Centre for Evolution and Cancer, The Institute of Cancer Research, London, UK.
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116
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Hua Y, Yang S, Zhang Y, Li J, Wang M, Yeerkenbieke P, Liao Q, Liu Q. Modulating ferroptosis sensitivity: environmental and cellular targets within the tumor microenvironment. J Exp Clin Cancer Res 2024; 43:19. [PMID: 38217037 PMCID: PMC10787430 DOI: 10.1186/s13046-023-02925-5] [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: 09/11/2023] [Accepted: 12/06/2023] [Indexed: 01/14/2024] Open
Abstract
Ferroptosis, a novel form of cell death triggered by iron-dependent phospholipid peroxidation, presents significant therapeutic potential across diverse cancer types. Central to cellular metabolism, the metabolic pathways associated with ferroptosis are discernible in both cancerous and immune cells. This review begins by delving into the intricate reciprocal regulation of ferroptosis between cancer and immune cells. It subsequently details how factors within the tumor microenvironment (TME) such as nutrient scarcity, hypoxia, and cellular density modulate ferroptosis sensitivity. We conclude by offering a comprehensive examination of distinct immunophenotypes and environmental and metabolic targets geared towards enhancing ferroptosis responsiveness within the TME. In sum, tailoring precise ferroptosis interventions and combination strategies to suit the unique TME of specific cancers may herald improved patient outcomes.
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Affiliation(s)
- Yuze Hua
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 1# Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Sen Yang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 1# Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Yalu Zhang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 1# Shuaifuyuan, Dongcheng District, Beijing, 100730, China
- Department of General Surgery, Anhui Provincial Hospital, Division of Life Science and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230027, China
| | - Jiayi Li
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 1# Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Mengyi Wang
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 1# Shuaifuyuan, Dongcheng District, Beijing, 100730, China
| | - Palashate Yeerkenbieke
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 1# Shuaifuyuan, Dongcheng District, Beijing, 100730, China
- Department of General Surgery, Xinjiang Yili Kazak Autonomous Prefecture Friendship Hospital, Xinjiang, 835099, China
| | - Quan Liao
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 1# Shuaifuyuan, Dongcheng District, Beijing, 100730, China.
| | - Qiaofei Liu
- Department of General Surgery, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 1# Shuaifuyuan, Dongcheng District, Beijing, 100730, China.
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117
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Liu SJ, Casey-Clyde T, Cho NW, Swinderman J, Pekmezci M, Dougherty MC, Foster K, Chen WC, Villanueva-Meyer JE, Swaney DL, Vasudevan HN, Choudhury A, Pak J, Breshears JD, Lang UE, Eaton CD, Hiam-Galvez KJ, Stevenson E, Chen KH, Lien BV, Wu D, Braunstein SE, Sneed PK, Magill ST, Lim D, McDermott MW, Berger MS, Perry A, Krogan NJ, Hansen MR, Spitzer MH, Gilbert L, Theodosopoulos PV, Raleigh DR. Epigenetic reprogramming shapes the cellular landscape of schwannoma. Nat Commun 2024; 15:476. [PMID: 38216587 PMCID: PMC10786948 DOI: 10.1038/s41467-023-40408-5] [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: 02/06/2023] [Accepted: 05/25/2023] [Indexed: 01/14/2024] Open
Abstract
Mechanisms specifying cancer cell states and response to therapy are incompletely understood. Here we show epigenetic reprogramming shapes the cellular landscape of schwannomas, the most common tumors of the peripheral nervous system. We find schwannomas are comprised of 2 molecular groups that are distinguished by activation of neural crest or nerve injury pathways that specify tumor cell states and the architecture of the tumor immune microenvironment. Moreover, we find radiotherapy is sufficient for interconversion of neural crest schwannomas to immune-enriched schwannomas through epigenetic and metabolic reprogramming. To define mechanisms underlying schwannoma groups, we develop a technique for simultaneous interrogation of chromatin accessibility and gene expression coupled with genetic and therapeutic perturbations in single-nuclei. Our results elucidate a framework for understanding epigenetic drivers of tumor evolution and establish a paradigm of epigenetic and metabolic reprograming of cancer cells that shapes the immune microenvironment in response to radiotherapy.
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Affiliation(s)
- S John Liu
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
- Arc Institute, Palo Alto, CA, 94304, USA
| | - Tim Casey-Clyde
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Nam Woo Cho
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Parker Institute for Cancer Immunotherapy, Chan Zuckerberg Biohub, and Departments of Otolaryngology, and Microbiology and Immunology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Jason Swinderman
- Arc Institute, Palo Alto, CA, 94304, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Melike Pekmezci
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Mark C Dougherty
- Departments of Otolaryngology and Neurosurgery, University of Iowa, Iowa City, IA, 52242, USA
| | - Kyla Foster
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - William C Chen
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Javier E Villanueva-Meyer
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, CA, USA
| | - Danielle L Swaney
- J. David Gladstone Institutes, California Institute for Quantitative Biosciences, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Harish N Vasudevan
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Abrar Choudhury
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Joanna Pak
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
- Arc Institute, Palo Alto, CA, 94304, USA
| | - Jonathan D Breshears
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Ursula E Lang
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Dermatology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Charlotte D Eaton
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Kamir J Hiam-Galvez
- Parker Institute for Cancer Immunotherapy, Chan Zuckerberg Biohub, and Departments of Otolaryngology, and Microbiology and Immunology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Erica Stevenson
- J. David Gladstone Institutes, California Institute for Quantitative Biosciences, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Kuei-Ho Chen
- J. David Gladstone Institutes, California Institute for Quantitative Biosciences, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Brian V Lien
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - David Wu
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Steve E Braunstein
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Penny K Sneed
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Stephen T Magill
- Department of Neurological Surgery, Northwestern University, Chicago, IL, 60611, USA
| | - Daniel Lim
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | | | - Mitchel S Berger
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Arie Perry
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Nevan J Krogan
- J. David Gladstone Institutes, California Institute for Quantitative Biosciences, Department of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA, 94158, USA
| | - Marlan R Hansen
- Departments of Otolaryngology and Neurosurgery, University of Iowa, Iowa City, IA, 52242, USA
| | - Matthew H Spitzer
- Parker Institute for Cancer Immunotherapy, Chan Zuckerberg Biohub, and Departments of Otolaryngology, and Microbiology and Immunology, University of California San Francisco, San Francisco, CA, 94115, USA
| | - Luke Gilbert
- Arc Institute, Palo Alto, CA, 94304, USA
- Department of Urology, University of California San Francisco, San Francisco, CA, 94143, USA
| | - Philip V Theodosopoulos
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA
| | - David R Raleigh
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, 94143, USA.
- Department of Neurological Surgery, University of California San Francisco, San Francisco, CA, 94143, USA.
- Department of Pathology, University of California San Francisco, San Francisco, CA, 94143, USA.
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Wu C, Tan J, Shen H, Deng C, Kleber C, Osterhoff G, Schopow N. Exploring the relationship between metabolism and immune microenvironment in osteosarcoma based on metabolic pathways. J Biomed Sci 2024; 31:4. [PMID: 38212768 PMCID: PMC10785352 DOI: 10.1186/s12929-024-00999-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND Metabolic remodeling and changes in tumor immune microenvironment (TIME) in osteosarcoma are important factors affecting prognosis and treatment. However, the relationship between metabolism and TIME needs to be further explored. METHODS RNA-Seq data and clinical information of 84 patients with osteosarcoma from the TARGET database and an independent cohort from the GEO database were included in this study. The activity of seven metabolic super-pathways and immune infiltration levels were inferred in osteosarcoma patients. Metabolism-related genes (MRGs) were identified and different metabolic clusters and MRG-related gene clusters were identified using unsupervised clustering. Then the TIME differences between the different clusters were compared. In addition, an MRGs-based risk model was constructed and the role of a key risk gene, ST3GAL4, in osteosarcoma cells was explored using molecular biological experiments. RESULTS This study revealed four key metabolic pathways in osteosarcoma, with vitamin and cofactor metabolism being the most relevant to prognosis and to TIME. Two metabolic pathway-related clusters (C1 and C2) were identified, with some differences in immune activating cell infiltration between the two clusters, and C2 was more likely to respond to two chemotherapeutic agents than C1. Three MRG-related gene clusters (GC1-3) were also identified, with significant differences in prognosis among the three clusters. GC2 and GC3 had higher immune cell infiltration than GC1. GC3 is most likely to respond to immune checkpoint blockade and to three commonly used clinical drugs. A metabolism-related risk model was developed and validated. The risk model has strong prognostic predictive power and the low-risk group has a higher level of immune infiltration than the high-risk group. Knockdown of ST3GAL4 significantly inhibited proliferation, migration, invasion and glycolysis of osteosarcoma cells and inhibited the M2 polarization of macrophages. CONCLUSION The metabolism of vitamins and cofactors is an important prognostic regulator of TIME in osteosarcoma, MRG-related gene clusters can well reflect changes in osteosarcoma TIME and predict chemotherapy and immunotherapy response. The metabolism-related risk model may serve as a useful prognostic predictor. ST3GAL4 plays a critical role in the progression, glycolysis, and TIME of osteosarcoma cells.
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Affiliation(s)
- Changwu Wu
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jun Tan
- Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Hong Shen
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Department of Oncology, Xiangya Hospital, Central South University, Changsha, Hunan, China.
- Key Laboratory for Molecular Radiation Oncology of Hunan Province, Xiangya Hospital, Central South University, Changsha, Hunan, China.
| | - Chao Deng
- Department of Orthopedics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Christian Kleber
- Sarcoma Center, Department of Orthopedics, Trauma and Plastic Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Georg Osterhoff
- Sarcoma Center, Department of Orthopedics, Trauma and Plastic Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Nikolas Schopow
- Sarcoma Center, Department of Orthopedics, Trauma and Plastic Surgery, University Hospital Leipzig, Leipzig, Germany
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Patz EF, Gottlin EB, Simon GR. Perspective: rethinking therapeutic strategies in oncology. Front Oncol 2024; 13:1335987. [PMID: 38269024 PMCID: PMC10805859 DOI: 10.3389/fonc.2023.1335987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024] Open
Abstract
Immuno-oncology has revolutionized cancer care, drug development, the design of clinical trials, standard treatment paradigms, and the evaluation of response to therapy. These are all areas, however, that have not fully incorporated principles of tumor immunology. Insufficient emphasis is put on the effect drugs have on the immune system, and specifically, the impact that multiple lines of therapy can have on the functioning of the immune system, hindering a robust anti-tumor immune response. A paradigm shift in how we approach the development of novel immunotherapeutic agents is necessary to facilitate the effective improvements in patient outcomes.
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Affiliation(s)
- Edward F. Patz
- Department of Radiology, Duke University School of Medicine, Durham, NC, United States
- Department of Pharmacology and Cancer Biology, Duke University School of Medicine, Durham, NC, United States
| | - Elizabeth B. Gottlin
- Department of Radiology, Duke University School of Medicine, Durham, NC, United States
| | - George R. Simon
- Department of Medical Oncology at Advent Health, Moffitt Cancer Center, Tampa, FL, United States
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Pellegrino S, Fonti R, Vallone C, Morra R, Matano E, De Placido S, Del Vecchio S. Coefficient of Variation in Metastatic Lymph Nodes Determined by 18F-FDG PET/CT in Patients with Advanced NSCLC: Combination with Coefficient of Variation in Primary Tumors. Cancers (Basel) 2024; 16:279. [PMID: 38254770 PMCID: PMC10813913 DOI: 10.3390/cancers16020279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/03/2024] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
Purpose The aim of the present study was to test whether the coefficient of variation (CoV) of 18F-FDG PET/CT images of metastatic lymph nodes and primary tumors may predict clinical outcome in patients with advanced non-small cell lung cancer (NSCLC). Materials and Methods Fifty-eight NSCLC patients who had undergone 18F-FDG PET/CT at diagnosis were evaluated. SUVmax, SUVmean, CoV, MTV and TLG were determined in targeted lymph nodes and corresponding primary tumors along with Total MTV (MTVTOT) and Whole-Body TLG (TLGWB) of all malignant lesions. Univariate analysis was performed using Cox proportional hazards regression whereas the Kaplan-Meier method and log-rank tests were used for survival analysis. Results Fifty-eight metastatic lymph nodes were analyzed and average values of SUVmax, SUVmean, CoV, MTV and TLG were 11.89 ± 8.54, 4.85 ± 1.90, 0.37 ± 0.16, 46.16 ± 99.59 mL and 256.84 ± 548.27 g, respectively, whereas in primary tumors they were 11.92 ± 6.21, 5.47 ± 2.34, 0.36 ± 0.14, 48.03 ± 64.45 mL and 285.21 ± 397.95 g, respectively. At univariate analysis, overall survival (OS) was predicted by SUVmax (p = 0.0363), SUVmean (p = 0.0200) and CoV (p = 0.0139) of targeted lymph nodes as well as by CoV of primary tumors (p = 0.0173), MTVTOT (p = 0.0007), TLGWB (p = 0.0129) and stage (p = 0.0122). Using Kaplan-Meier analysis, OS was significantly better in patients with CoV of targeted lymph nodes ≤ 0.29 than those with CoV > 0.29 (p = 0.0147), meanwhile patients with CoV of primary tumors > 0.38 had a better prognosis compared to those with CoV ≤ 0.38 (p = 0.0137). Finally, we combined the CoV values of targeted lymph nodes and primary tumors in all possible arrangements and a statistically significant difference was found among the four survival curves (p = 0.0133). In particular, patients with CoV of targeted lymph nodes ≤ 0.29 and CoV of primary tumors > 0.38 had the best prognosis. Conclusions The CoV of targeted lymph nodes combined with the CoV of primary tumors can predict prognosis of NSCLC patients.
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Affiliation(s)
- Sara Pellegrino
- Department of Advanced Biomedical Sciences, University of Naples “Federico II”, 80131 Naples, Italy; (S.P.); (R.F.); (C.V.)
| | - Rosa Fonti
- Department of Advanced Biomedical Sciences, University of Naples “Federico II”, 80131 Naples, Italy; (S.P.); (R.F.); (C.V.)
| | - Carlo Vallone
- Department of Advanced Biomedical Sciences, University of Naples “Federico II”, 80131 Naples, Italy; (S.P.); (R.F.); (C.V.)
| | - Rocco Morra
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80131 Naples, Italy; (R.M.); (E.M.); (S.D.P.)
| | - Elide Matano
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80131 Naples, Italy; (R.M.); (E.M.); (S.D.P.)
| | - Sabino De Placido
- Department of Clinical Medicine and Surgery, University of Naples “Federico II”, 80131 Naples, Italy; (R.M.); (E.M.); (S.D.P.)
| | - Silvana Del Vecchio
- Department of Advanced Biomedical Sciences, University of Naples “Federico II”, 80131 Naples, Italy; (S.P.); (R.F.); (C.V.)
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Liu D, Che X, Wu G. Deciphering the role of neddylation in tumor microenvironment modulation: common outcome of multiple signaling pathways. Biomark Res 2024; 12:5. [PMID: 38191508 PMCID: PMC10773064 DOI: 10.1186/s40364-023-00545-x] [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: 08/15/2023] [Accepted: 11/10/2023] [Indexed: 01/10/2024] Open
Abstract
Neddylation is a post-translational modification process, similar to ubiquitination, that controls several biological processes. Notably, it is often aberrantly activated in neoplasms and plays a critical role in the intricate dynamics of the tumor microenvironment (TME). This regulatory influence of neddylation permeates extensively and profoundly within the TME, affecting the behavior of tumor cells, immune cells, angiogenesis, and the extracellular matrix. Usually, neddylation promotes tumor progression towards increased malignancy. In this review, we highlight the latest understanding of the intricate molecular mechanisms that target neddylation to modulate the TME by affecting various signaling pathways. There is emerging evidence that the targeted disruption of the neddylation modification process, specifically the inhibition of cullin-RING ligases (CRLs) functionality, presents a promising avenue for targeted therapy. MLN4924, a small-molecule inhibitor of the neddylation pathway, precisely targets the neural precursor cell-expressed developmentally downregulated protein 8 activating enzyme (NAE). In recent years, significant advancements have been made in the field of neddylation modification therapy, particularly the integration of MLN4924 with chemotherapy or targeted therapy. This combined approach has demonstrated notable success in the treatment of a variety of hematological and solid tumors. Here, we investigated the inhibitory effects of MLN4924 on neddylation and summarized the current therapeutic outcomes of MLN4924 against various tumors. In conclusion, this review provides a comprehensive, up-to-date, and thorough overview of neddylation modifications, and offers insight into the critical importance of this cellular process in tumorigenesis.
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Affiliation(s)
- Dequan Liu
- Department of Urology, the First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China
| | - Xiangyu Che
- Department of Urology, the First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China.
| | - Guangzhen Wu
- Department of Urology, the First Affiliated Hospital of Dalian Medical University, Dalian, 116011, China.
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Kam NW, Lo AWI, Hung DTY, Ko H, Wu KC, Kwong DLW, Lam KO, Leung TW, Che CM, Lee VHF. Shift in Tissue-Specific Immune Niches and CD137 Expression in Tuberculoma of Pembrolizumab-Treated Nasopharyngeal Carcinoma Patients. Cancers (Basel) 2024; 16:268. [PMID: 38254759 PMCID: PMC10813936 DOI: 10.3390/cancers16020268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/24/2024] Open
Abstract
The use of immune checkpoint inhibitors (ICIs) in cancer treatment has shown promise but can also have unintended consequences, such as reactivating latent tuberculosis (TB). To develop treatments that address ICIs-related adverse events, it is essential to understand cellular heterogeneity across healthy and pathological tissues. We performed cross-tissue multiplexed staining analysis on samples from two patients with TB reactivation during pembrolizumab treatment for metastatic nasopharyngeal carcinoma. CD8+ T cells, rather than CD4+ T cells, accumulated preferentially in the tuberculoma and were associated with increased production of IFNγ and expression of CD137. Additionally, CD137 enrichment played a role in the spatial organization of the tuberculoma, with specific interaction limited to spatial proximal cells between IFNγ+ CD137+ CD8+ T cells and IL12+ CD137+ type-1 macrophages. This unique feature was not observed in non-tumoral or tumoral tissues. Our analysis of public transcriptomic datasets supported the notion that this cellular interaction was more prominent in patients with durable ICI responses compared to those with non-ICI-related TB. We suggest that shifts towards CD137-rich immune niches are correlated with both off-target immune-related adverse events and anti-tumor efficacy. Targeting the tumor microenvironment through conditional activation of anti-CD137 signaling in combination with ICIs can modulate the reactivity of T cells and macrophages for localized tumor killing without the potential off-target immune-related risks associated with ICIs alone.
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Affiliation(s)
- Ngar Woon Kam
- Department of Clinical Oncology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.W.K.); (D.T.Y.H.); (K.C.W.); (D.L.W.K.); (K.O.L.); (T.W.L.)
- Laboratory of Synthetic Chemistry and Chemical Biology Limited, Hong Kong 999077, China;
| | | | - Desmond Tae Yang Hung
- Department of Clinical Oncology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.W.K.); (D.T.Y.H.); (K.C.W.); (D.L.W.K.); (K.O.L.); (T.W.L.)
| | - Ho Ko
- Department of Medicine and Therapeutics, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China;
- Li Ka Shing Institute of Health Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, Hong Kong 999077, China
| | - Ka Chun Wu
- Department of Clinical Oncology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.W.K.); (D.T.Y.H.); (K.C.W.); (D.L.W.K.); (K.O.L.); (T.W.L.)
- Laboratory of Synthetic Chemistry and Chemical Biology Limited, Hong Kong 999077, China;
| | - Dora Lai Wan Kwong
- Department of Clinical Oncology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.W.K.); (D.T.Y.H.); (K.C.W.); (D.L.W.K.); (K.O.L.); (T.W.L.)
- Clinical Oncology Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518000, China
| | - Ka On Lam
- Department of Clinical Oncology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.W.K.); (D.T.Y.H.); (K.C.W.); (D.L.W.K.); (K.O.L.); (T.W.L.)
- Clinical Oncology Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518000, China
| | - To Wai Leung
- Department of Clinical Oncology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.W.K.); (D.T.Y.H.); (K.C.W.); (D.L.W.K.); (K.O.L.); (T.W.L.)
| | - Chi Ming Che
- Laboratory of Synthetic Chemistry and Chemical Biology Limited, Hong Kong 999077, China;
- Department of Chemistry, Faculty of Science, The University of Hong Kong, Hong Kong 999077, China
| | - Victor Ho Fun Lee
- Department of Clinical Oncology, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (N.W.K.); (D.T.Y.H.); (K.C.W.); (D.L.W.K.); (K.O.L.); (T.W.L.)
- Clinical Oncology Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518000, China
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Cai Y, Liu S, Zhao X, Ren L, Liu X, Gang X, Wang G. Pathogenesis, clinical features, and treatment of plurihormonal pituitary adenoma. Front Neurosci 2024; 17:1323883. [PMID: 38260014 PMCID: PMC10800528 DOI: 10.3389/fnins.2023.1323883] [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: 10/18/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Plurihormonal pituitary adenoma (PPA) is a type of pituitary tumor capable of producing two or more hormones and usually presents as an aggressive, large adenoma. As yet, its pathogenesis remains unclear. This is the first study to systematically summarize the underlying pathogenesis of PPA. The pathogenesis is related to plurihormonal primordial stem cells, co-transcription factors, hormone co-expression, differential gene expression, and cell transdifferentiation. We conducted a literature review of PPA and analyzed its clinical characteristics. We found that the average age of patients with PPA was approximately 40 years, and most showed only one clinical symptom. The most common manifestation was acromegaly. Currently, PPA is treated with surgical resection. However, recent studies suggest that immunotherapy may be a potentially effective treatment.
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Affiliation(s)
| | | | | | | | | | - Xiaokun Gang
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, China
| | - Guixia Wang
- Department of Endocrinology and Metabolism, The First Hospital of Jilin University, Changchun, China
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Bouchnita A, Volpert V. Phenotype-structured model of intra-clonal heterogeneity and drug resistance in multiple myeloma. J Theor Biol 2024; 576:111652. [PMID: 37952610 DOI: 10.1016/j.jtbi.2023.111652] [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: 07/24/2023] [Revised: 09/26/2023] [Accepted: 10/22/2023] [Indexed: 11/14/2023]
Abstract
Multiple myeloma (MM) is a genetically complex hematological cancer characterized by the abnormal proliferation of malignant plasma cells in the bone marrow. This disease progresses from a premalignant condition known as monoclonal gammopathy of unknown significance (MGUS) through sequential genetic alterations involving various genes. These genetic changes contribute to the uncontrolled growth of multiple clones of plasma cells. In this study, we present a phenotype-structured model that captures the intra-clonal heterogeneity and drug resistance in multiple myeloma (MM). The model accurately reproduces the branching evolutionary pattern observed in MM progression, aligning with a previously developed multiscale model. Numerical simulations reveal that higher mutation rates enhance tumor phenotype diversity, while access to growth factors accelerates tumor evolution and increases its final size. Interestingly, the model suggests that further increasing growth factor access primarily amplifies tumor size rather than altering clonal dynamics. Additionally, the model emphasizes that higher mutation frequencies and growth factor availability elevate the chances of drug resistance and relapse. It indicates that the timing of the treatment could trajectory of tumor evolution and clonal emergence in the case of branching evolutionary pattern. Given its low computational cost, our model is well-suited for quantitative studies on MM clonal heterogeneity and its interaction with chemotherapeutic treatments.
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Affiliation(s)
- Anass Bouchnita
- Department of Mathematical Sciences, The University of Texas at El Paso, El Paso, 79968, TX, United States.
| | - Vitaly Volpert
- Institut Camille Jordan, UMR 5208 CNRS, University Lyon 1, 69622 Villeurbanne, France; Peoples Friendship University of Russia (RUDN University), 6 Miklukho-Maklaya St, 117198 Moscow, Russian Federation
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125
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Baygin RC, Yilmaz KC, Acar A. Characterization of dabrafenib-induced drug insensitivity via cellular barcoding and collateral sensitivity to second-line therapeutics. Sci Rep 2024; 14:286. [PMID: 38167959 PMCID: PMC10762103 DOI: 10.1038/s41598-023-50443-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
Drug insensitivity is arguably one of the biggest challenges in cancer therapeutics. Although effective therapeutic solutions in cancer are limited due to the emergence of drug insensitivity, exploiting evolutionary understanding in this context can provide potential second-line therapeutics sensitizing the drug insensitive populations. Targeted therapeutic agent dabrafenib is used to treat CRC patients with BRAF V600E genotype and insensitivity to dabrafenib is often observed. Understanding underlying clonal architecture of dabrafenib-induced drug insensitivity and identification of potential second-line therapeutics that could sensitize dabrafenib insensitive populations remain to be elucidated. For this purpose, we utilized cellular barcoding technology to decipher dabrafenib-induced clonal evolution in BRAF V600E mutant HT-29 cells. This approach revealed the detection of both pre-existing and de novo barcodes with increased frequencies as a result of dabrafenib insensitivity. Furthermore, our longitudinal monitoring of drug insensitivity based on barcode detection from floating DNA within used medium enabled to identify temporal dynamics of pre-existing and de novo barcodes in relation to dabrafenib insensitivity in HT-29 cells. Moreover, whole-exome sequencing analysis exhibited possible somatic CNVs and SNVs contributing to dabrafenib insensitivity in HT-29 cells. Last, collateral drug sensitivity testing demonstrated oxaliplatin and capecitabine, alone or in combination, as successful second-like therapeutics in inducing collateral sensitivity in dabrafenib-insensitive HT-29 cells. Overall, our findings demonstrate clonal dynamics of dabrafenib-insensitivity in HT-29 cells. In addition, oxaliplatin and capecitabine, alone or in combination, were successful second-line therapeutics in inducing collateral sensitivity in dabrafenib-insensitive HT-29 cells.
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Affiliation(s)
- Rana Can Baygin
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupınar Bulvarı 1, Çankaya, 06800, Ankara, Turkey
| | - Kubra Celikbas Yilmaz
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupınar Bulvarı 1, Çankaya, 06800, Ankara, Turkey
| | - Ahmet Acar
- Department of Biological Sciences, Middle East Technical University, Universiteler Mah. Dumlupınar Bulvarı 1, Çankaya, 06800, Ankara, Turkey.
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Ohyama H, Hirotsu Y, Amemiya K, Mikata R, Amano H, Hirose S, Oyama T, Iimuro Y, Kojima Y, Mochizuki H, Kato N, Omata M. Development of a molecular barcode detection system for pancreaticobiliary malignancies and comparison with next-generation sequencing. Cancer Genet 2024; 280-281:6-12. [PMID: 38113555 DOI: 10.1016/j.cancergen.2023.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Revised: 10/29/2023] [Accepted: 12/07/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND Obtaining sufficient tumor tissue for genomic profiling is challenging in pancreaticobiliary cancer (PBCA). We determined the utility of molecular barcoding (MB) of liquid biopsies (bile, duodenal fluid, and plasma) for highly sensitive genomic diagnosis and detection of druggable mutations for PBCA. METHODS Two in-house panels of 60 genes (non-MB panel) and 21 genes using MB (MB panel) were used for the genomic analysis of 112 DNA samples from 20 PBCA patients. We measured the yield of DNA and compared the genomic profiles of liquid samples obtained using the non-MB panel and the MB panel. The utility of the panels in detecting druggable mutations was investigated. RESULTS A significantly greater amount of DNA was obtained from bile supernatants and precipitates compared to tumor samples (P < 0.001 and P = 0.001, respectively). The number of mutations per patient was significantly higher using the MB panel than using the non-MB panel (2.8 vs. 1.3, P = 0.002). Tumor-derived mutations were detected more frequently using the MB panel than the non-MB panel (P = 0.023). Five drug-matched mutations were detected in liquid samples. CONCLUSIONS Liquid biopsy with MB may have utility in providing genomic information for the prognosis of patients with PBCA.
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Affiliation(s)
- Hiroshi Ohyama
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan; Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan; Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan.
| | - Yosuke Hirotsu
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Kenji Amemiya
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan
| | - Rintaro Mikata
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Hiroyuki Amano
- Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Sumio Hirose
- Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Toshio Oyama
- Department of Pathology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yuji Iimuro
- Department of Surgery, Yamanashi Central Hospital, Yamanashi, Japan
| | - Yuichiro Kojima
- Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Hitoshi Mochizuki
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan; Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan
| | - Naoya Kato
- Department of Gastroenterology, Graduate School of Medicine, Chiba University, Chiba, Japan
| | - Masao Omata
- Genome Analysis Center, Yamanashi Central Hospital, Yamanashi, Japan; Department of Gastroenterology, Yamanashi Central Hospital, Yamanashi, Japan; University of Tokyo, Tokyo, Japan
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Ge LP, Jin X, Ma D, Wang ZY, Liu CL, Zhou CZ, Zhao S, Yu TJ, Liu XY, Di GH, Shao ZM, Jiang YZ. ZNF689 deficiency promotes intratumor heterogeneity and immunotherapy resistance in triple-negative breast cancer. Cell Res 2024; 34:58-75. [PMID: 38168642 PMCID: PMC10770380 DOI: 10.1038/s41422-023-00909-w] [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: 02/26/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive disease characterized by remarkable intratumor heterogeneity (ITH), which poses therapeutic challenges. However, the clinical relevance and key determinant of ITH in TNBC are poorly understood. Here, we comprehensively characterized ITH levels using multi-omics data across our center's cohort (n = 260), The Cancer Genome Atlas cohort (n = 134), and four immunotherapy-treated cohorts (n = 109). Our results revealed that high ITH was associated with poor patient survival and immunotherapy resistance. Importantly, we identified zinc finger protein 689 (ZNF689) deficiency as a crucial determinant of ITH formation. Mechanistically, the ZNF689-TRIM28 complex was found to directly bind to the promoter of long interspersed element-1 (LINE-1), inducing H3K9me3-mediated transcriptional silencing. ZNF689 deficiency reactivated LINE-1 retrotransposition to exacerbate genomic instability, which fostered ITH. Single-cell RNA sequencing, spatially resolved transcriptomics and flow cytometry analysis confirmed that ZNF689 deficiency-induced ITH inhibited antigen presentation and T-cell activation, conferring immunotherapy resistance. Pharmacological inhibition of LINE-1 significantly reduced ITH, enhanced antitumor immunity, and eventually sensitized ZNF689-deficient tumors to immunotherapy in vivo. Consistently, ZNF689 expression positively correlated with favorable prognosis and immunotherapy response in clinical samples. Altogether, our study uncovers a previously unrecognized mechanism underlying ZNF689 deficiency-induced ITH and suggests LINE-1 inhibition combined with immunotherapy as a novel treatment strategy for TNBC.
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Affiliation(s)
- Li-Ping Ge
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Xi Jin
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Ding Ma
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zi-Yu Wang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Cheng-Lin Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Chao-Zheng Zhou
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shen Zhao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tian-Jian Yu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xi-Yu Liu
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Gen-Hong Di
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Zhi-Ming Shao
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
- Human Phenome Institute, Fudan University, Shanghai, China.
| | - Yi-Zhou Jiang
- Key Laboratory of Breast Cancer in Shanghai, Department of Breast Surgery, Precision Cancer Medicine Center, Fudan University Shanghai Cancer Center, Shanghai, China.
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.
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Thakkar PV. Immunoblot Analysis from Single Cells Using Milo™ Single-Cell Western Platform. Methods Mol Biol 2024; 2752:201-214. [PMID: 38194036 DOI: 10.1007/978-1-0716-3621-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
In this new era of precision medicine, characterization of single-cell subpopulations to better understand disease etiology is paramount. It is thus an opportune time to explore techniques that allow molecular analysis of single cells and to better understand the basis of pathogenesis of diseases like cancer. Single-cell western blotting is one such method that allows analysis of single cells at the protein level. In contrast to traditional western blotting, which relies heavily on bulk analysis of lysates generated from tissues and is often indicative of the population average, this technique allows analysis of lysates from single-cell subpopulations thereby providing a glimpse into cell heterogeneity. The method entails the use of a chip containing 30 μm thick photoactivated polyacrylamide gel spotted with nearly 6400 microwells. Single cells loaded on the chip are captured in the microwells by passive gravity and are then lysed and electrophoresed using the MILO™ single-cell western platform. This method forgoes the use of transfer of proteins on a PVDF and a nitrocellulose membrane, as performed in traditional western blotting, and all other steps including probing of primary and fluorescent secondary antibodies against the protein of interest are performed directly on the chip. The proteins of interest can then be visualized by scanning a chip with the use of a microarray scanner. The entire procedure can be performed in as less as 4-6 h, and thus this method provides several advantages over traditional western blotting.
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Affiliation(s)
- Prashant V Thakkar
- Department of Hematology and Medical Oncology, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
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129
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Gristina V, Malapelle U. Dissecting the nuances of cancer epigenomics in liquid biopsy. Epigenomics 2024; 16:79-83. [PMID: 38166432 DOI: 10.2217/epi-2023-0326] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2024] Open
Affiliation(s)
- Valerio Gristina
- Department of Surgical, Oncological & Oral Sciences, University of Palermo, Palermo, 90127, Italy
| | - Umberto Malapelle
- Department of Public Health, University Federico II of Naples, Naples, 80131, Italy
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130
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Mishra R. Oral tumor heterogeneity, its implications for patient monitoring and designing anti-cancer strategies. Pathol Res Pract 2024; 253:154953. [PMID: 38039738 DOI: 10.1016/j.prp.2023.154953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 12/03/2023]
Abstract
Oral cancer tumors occur in the mouth and are mainly derived from oral mucosa linings. It is one of the most common and fatal malignant diseases worldwide. The intratumor heterogeneity (ITH) of oral cancerous tumor is vast, so it is challenging to study and interpret. Due to environmental selection pressures, ITH arises through diverse genetic, epigenetic, and metabolic alterations. The ITH also talks about peri-tumoral vascular/ lymphatic growth, perineural permeation, tumor necrosis, invasion, and clonal expansion/ the coexistence of multiple subclones in a single tumor. The heterogeneity offers tumors the adaptability to survive, induce growth/ metastasis, and, most importantly, escape antitumor therapy. Unfortunately, the ITH is prioritized less in determining disease pathology than the traditional TNM classifications or tumor grade. Understanding ITH is challenging, but with the advancement of technology, this ITH can be decoded. Tumor genomics, proteomics, metabolomics, and other modern analyses can provide vast information. This information in clinics can assist in understanding a tumor's severity and be used for diagnostic, prognostic, and therapeutic decision-making. Lastly, the oral tumor ITH can lead to individualized, targeted therapy strategies fighting against OC.
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Affiliation(s)
- Rajakishore Mishra
- Department of Life Sciences, School of Natural Sciences, Central University of Jharkhand, Cheri-Manatu, Kamre, Ranchi 835 222, Jharkhand, India.
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131
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Gao Y, Zhou N, Liu J. Ovarian Cancer Diagnosis and Prognosis Based on Cell-Free DNA Methylation. Cancer Control 2024; 31:10732748241255548. [PMID: 38764160 PMCID: PMC11104031 DOI: 10.1177/10732748241255548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/12/2024] [Accepted: 04/30/2024] [Indexed: 05/21/2024] Open
Abstract
Background: Ovarian cancer stands as the deadliest malignant tumor within the female reproductive tract. As a result of the absence of effective diagnostic and monitoring markers, 75% of ovarian cancer cases are diagnosed at a late stage, leading to a mere 50% survival rate within five years. The advancement of molecular biology is essential for accurate diagnosis and treatment of ovarian cancer. Methods: A review of several randomized clinical trials, focusing on the ovarian cancer, was undertaken. The advancement of molecular biology and diagnostic methods related to accurate diagnosis and treatment of ovarian cancer were examined. Results: Liquid biopsy is an innovative method of detecting malignant tumors that has gained increasing attention over the past few years. Cell-free DNA assay-based liquid biopsies show potential in delineating tumor status heterogeneity and tracking tumor recurrence. DNA methylation influences a multitude of biological functions and diseases, especially during the initial phases of cancer. The cell-free DNA methylation profiling system has emerged as a sensitive and non-invasive technique for identifying and detecting the biological origins of cancer. It holds promise as a biomarker, enabling early screening, recurrence monitoring, and prognostic evaluation of cancer. Conclusions: This review evaluates recent advancements and challenges associated with cell-free DNA methylation analysis for the diagnosis, prognosis monitoring, and assessment of therapeutic responses in the management of ovarian cancers, aiming to offer guidance for precise diagnosis and treatment of this disease.
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Affiliation(s)
- Yajuan Gao
- Department of Gynecology and Obstetrics, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Nanyang Zhou
- Department of Traditional Chinese Medicine, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Jie Liu
- Department of Gynecology and Obstetrics, Hangzhou Women’s Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
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Sadida HQ, Abdulla A, Marzooqi SA, Hashem S, Macha MA, Akil ASAS, Bhat AA. Epigenetic modifications: Key players in cancer heterogeneity and drug resistance. Transl Oncol 2024; 39:101821. [PMID: 37931371 PMCID: PMC10654239 DOI: 10.1016/j.tranon.2023.101821] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Revised: 10/12/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023] Open
Abstract
Cancer heterogeneity and drug resistance remain pivotal obstacles in effective cancer treatment and management. One major contributor to these challenges is epigenetic modifications - gene regulation that does not involve changes to the DNA sequence itself but significantly impacts gene expression. As we elucidate these phenomena, we underscore the pivotal role of epigenetic modifications in regulating gene expression, contributing to cellular diversity, and driving adaptive changes that can instigate therapeutic resistance. This review dissects essential epigenetic modifications - DNA methylation, histone modifications, and chromatin remodeling - illustrating their significant yet complex contributions to cancer biology. While these changes offer potential avenues for therapeutic intervention due to their reversible nature, the interplay of epigenetic and genetic changes in cancer cells presents unique challenges that must be addressed to harness their full potential. By critically analyzing the current research landscape, we identify knowledge gaps and propose future research directions, exploring the potential of epigenetic therapies and discussing the obstacles in translating these concepts into effective treatments. This comprehensive review aims to stimulate further research and aid in developing innovative, patient-centered cancer therapies. Understanding the role of epigenetic modifications in cancer heterogeneity and drug resistance is critical for scientific advancement and paves the way towards improving patient outcomes in the fight against this formidable disease.
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Affiliation(s)
- Hana Q Sadida
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Alanoud Abdulla
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Sara Al Marzooqi
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Sheema Hashem
- Laboratory of Genomic Medicine, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar
| | - Muzafar A Macha
- Watson-Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Jammu & Kashmir, India
| | - Ammira S Al-Shabeeb Akil
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar.
| | - Ajaz A Bhat
- Laboratory of Precision Medicine in Diabetes, Obesity and Cancer, Department of Population Genetics, Sidra Medicine, Doha 26999, Qatar.
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Lin Y, Ho C, Hsu W, Liao W, Yang C, Yu C, Tsai T, Yang JC, Wu S, Hsu C, Hsieh M, Huang Y, Wu C, Shih J. Tissue or liquid rebiopsy? A prospective study for simultaneous tissue and liquid NGS after first-line EGFR inhibitor resistance in lung cancer. Cancer Med 2024; 13:e6870. [PMID: 38140788 PMCID: PMC10807591 DOI: 10.1002/cam4.6870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 11/28/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
INTRODUCTION According to current International Association for the Study of Lung Cancer guideline, physicians may first use plasma cell-free DNA (cfDNA) methods to identify epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI)-resistant mechanisms (liquid rebiopsy) for lung cancer. Tissue rebiopsy is recommended if the plasma result is negative. However, this approach has not been evaluated prospectively using next-generation sequencing (NGS). METHODS We prospectively enrolled patients with lung cancer with first-line EGFR-TKI resistance who underwent tissue rebiopsy. The rebiopsied tissues and cfDNA were sequenced using targeted NGS, ACTDrug®+, and ACTMonitor®Lung simultaneously. The clinicopathological characteristics and treatment outcomes were analyzed. RESULTS Totally, 86 patients were enrolled. Twenty-six (30%) underwent tissue biopsy but the specimens were inadequate for NGS. Among the 60 patients with paired tissue and liquid rebiopsies, two-thirds (40/60) may still be targetable. T790M mutations were found in 29, including 14 (48%) only from tissue and 5 (17%) only from cfDNA. Twenty-four of them were treated with osimertinib, and progression-free survival was longer in patients without detectable T790M in cfDNA than in patients with detectable T790M in cfDNA (p = 0.02). For the 31 T790M-negative patients, there were six with mesenchymal-epithelial transition factor (MET) amplifications, four with ERBB2 amplifications, and one with CCDC6-RET fusion. One with MET amplification and one with ERBB2 amplification responded to subsequent MET and ERBB2 targeting agents respectively. CONCLUSIONS NGS after EGFR-TKI resistance may detect targetable drivers besides T790M. To do either liquid or tissue NGS only could miss patients with T790M. To do tissue and liquid NGS in parallel after EGFR-TKI resistance may find more patients with targetable cancers.
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Affiliation(s)
- Yen‐Ting Lin
- Graduate Institute of Clinical MedicineNational Taiwan University College of MedicineTaipeiTaiwan
- Department of MedicineNational Taiwan University Cancer CenterTaipeiTaiwan
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - Chao‐Chi Ho
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - Wei‐Hsun Hsu
- Department of Medical ResearchNational Taiwan University HospitalTaipeiTaiwan
| | - Wei‐Yu Liao
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - Ching‐Yao Yang
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - Chong‐Jen Yu
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
- Department of Internal MedicineNational Taiwan University Hospital Hsin‐Chu BranchHsin‐ChuTaiwan
| | - Tzu‐Hsiu Tsai
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - James Chih‐Hsin Yang
- Department of Medical OncologyNational Taiwan University Cancer CenterTaipeiTaiwan
- Department of OncologyNational Taiwan University HospitalTaipeiTaiwan
- Graduate Institute of OncologyNational Taiwan University College of MedicineTaipeiTaiwan
| | - Shang‐Gin Wu
- Department of MedicineNational Taiwan University Cancer CenterTaipeiTaiwan
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - Chia‐Lin Hsu
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
| | - Min‐Shu Hsieh
- Department of PathologyNational Taiwan University HospitalTaipeiTaiwan
- Department of PathologyNational Taiwan University Cancer CenterTaipeiTaiwan
| | - Yen‐Lin Huang
- Department of PathologyNational Taiwan University Cancer CenterTaipeiTaiwan
| | | | - Jin‐Yuan Shih
- Graduate Institute of Clinical MedicineNational Taiwan University College of MedicineTaipeiTaiwan
- Department of Internal MedicineNational Taiwan University Hospital and National Taiwan University College of MedicineTaipeiTaiwan
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134
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Musella M, Manduca N, Maccafeo E, Ruggiero E, Sistigu A. In Vitro Evaluation of Cancer Cell Immunogenicity and Antigen-Specific T-Cell Cytotoxicity by Flow Cytometry. Methods Mol Biol 2024; 2748:13-28. [PMID: 38070104 DOI: 10.1007/978-1-0716-3593-3_2] [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: 12/18/2023]
Abstract
A cardinal principle of oncoimmunology is that cancer cells can be eliminated by tumor-infiltrating cytotoxic CD8 T lymphocytes. This has been widely demonstrated during the last 20 years and also recently harnessed for therapy. However, emerging evidence indicates that even neoplasms showing striking initial responses to conventional and targeted (immuno)therapies often acquire resistance, resulting in tumor relapse, increased aggressiveness, and metastatization. Indeed, tumors are complex ecosystems whose malignant and nonmalignant cells, constituting the tumor microenvironment, constantly interact and evolve in space and time. Together with patient's own genetic factors, such environmental interplays may curtail antitumor immune responses leading to cancer immune evasion and natural/acquired (immuno)therapy resistance. In this context, cancer stem cells (CSCs) are thought to be the roots of therapy failure. Flow cytometry is a powerful technology that finds extensive applications in cancer biology. It offers several unique advantages as it allows the rapid, quantitative, and multiparametric analysis of cell populations or functions at the single-cell level. In this chapter, we discuss a two-color flow cytometric protocol to evaluate cancer cell immunogenicity by analyzing the proliferative and tumor-killing potential of ovalbumin (OVA)-specific CD8 OT-1 T cells exposed to OVA-expressing MCA205 sarcoma cells and their CSC counterparts.
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Affiliation(s)
- Martina Musella
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy.
| | - Nicoletta Manduca
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Ester Maccafeo
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Eliana Ruggiero
- Experimental Hematology Unit, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Antonella Sistigu
- Dipartimento di Medicina e Chirurgia Traslazionale, Università Cattolica del Sacro Cuore, Rome, Italy.
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135
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Ngo HKC, Le H, Surh YJ. Nrf2, A Target for Precision Oncology in Cancer Prognosis and Treatment. J Cancer Prev 2023; 28:131-142. [PMID: 38205365 PMCID: PMC10774478 DOI: 10.15430/jcp.2023.28.4.131] [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: 12/15/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Activating nuclear factor-erythroid 2-related factor (Nrf2), a master regulator of redox homeostasis, has been shown to suppress initiation of carcinogenesis in normal cells. However, this transcription factor has recently been reported to promote proliferation of some transformed or cancerous cells. In tumor cells, Nrf2 is prone to mutations that result in stabilization and concurrent accumulation of its protein product. A hyperactivated mutant form of Nrf2 could support the cancer cells for enhanced proliferation, invasiveness, and resistance to chemotherapeutic agents and radiotherapy, which are associated with a poor clinical outcome. Hence understanding mutations in Nrf2 would have a significant impact on the prognosis and treatment of cancer in the era of precision medicine. This perspective would provide an insight into the genetic alterations in Nrf2 and suggest the application of small molecules, RNAi, and genome editing technologies, particularly CRISR-Cas9, in therapeutic intervention of cancer in the context of the involvement of Nrf2 mutations.
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Affiliation(s)
- Hoang Kieu Chi Ngo
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, Korea
| | - Hoang Le
- Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Charlestown, MA, USA
| | - Young-Joon Surh
- Tumor Microenvironment Global Core Research Center, College of Pharmacy, Seoul National University, Seoul, Korea
- Cancer Research Institute, Seoul National University, Seoul, Korea
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Melton CA, Freese P, Zhou Y, Shenoy A, Bagaria S, Chang C, Kuo CC, Scott E, Srinivasan S, Cann G, Roychowdhury-Saha M, Chang PY, Singh AH. A Novel Tissue-Free Method to Estimate Tumor-Derived Cell-Free DNA Quantity Using Tumor Methylation Patterns. Cancers (Basel) 2023; 16:82. [PMID: 38201510 PMCID: PMC10777919 DOI: 10.3390/cancers16010082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/20/2023] [Indexed: 01/12/2024] Open
Abstract
Estimating the abundance of cell-free DNA (cfDNA) fragments shed from a tumor (i.e., circulating tumor DNA (ctDNA)) can approximate tumor burden, which has numerous clinical applications. We derived a novel, broadly applicable statistical method to quantify cancer-indicative methylation patterns within cfDNA to estimate ctDNA abundance, even at low levels. Our algorithm identified differentially methylated regions (DMRs) between a reference database of cancer tissue biopsy samples and cfDNA from individuals without cancer. Then, without utilizing matched tissue biopsy, counts of fragments matching the cancer-indicative hyper/hypo-methylated patterns within DMRs were used to determine a tumor methylated fraction (TMeF; a methylation-based quantification of the circulating tumor allele fraction and estimate of ctDNA abundance) for plasma samples. TMeF and small variant allele fraction (SVAF) estimates of the same cancer plasma samples were correlated (Spearman's correlation coefficient: 0.73), and synthetic dilutions to expected TMeF of 10-3 and 10-4 had estimated TMeF within two-fold for 95% and 77% of samples, respectively. TMeF increased with cancer stage and tumor size and inversely correlated with survival probability. Therefore, tumor-derived fragments in the cfDNA of patients with cancer can be leveraged to estimate ctDNA abundance without the need for a tumor biopsy, which may provide non-invasive clinical approximations of tumor burden.
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137
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Imran H, Tang Y, Wang S, Yan X, Liu C, Guo L, Wang E, Xu C. Optimized DOX Drug Deliveries via Chitosan-Mediated Nanoparticles and Stimuli Responses in Cancer Chemotherapy: A Review. Molecules 2023; 29:31. [PMID: 38202616 PMCID: PMC10780101 DOI: 10.3390/molecules29010031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 01/12/2024] Open
Abstract
Chitosan nanoparticles (NPs) serve as useful multidrug delivery carriers in cancer chemotherapy. Chitosan has considerable potential in drug delivery systems (DDSs) for targeting tumor cells. Doxorubicin (DOX) has limited application due to its resistance and lack of specificity. Chitosan NPs have been used for DOX delivery because of their biocompatibility, biodegradability, drug encapsulation efficiency, and target specificity. In this review, various types of chitosan derivatives are discussed in DDSs to enhance the effectiveness of cancer treatments. Modified chitosan-DOX NP drug deliveries with other compounds also increase the penetration and efficiency of DOX against tumor cells. We also highlight the endogenous stimuli (pH, redox, enzyme) and exogenous stimuli (light, magnetic, ultrasound), and their positive effect on DOX drug delivery via chitosan NPs. Our study sheds light on the importance of chitosan NPs for DOX drug delivery in cancer treatment and may inspire the development of more effective approaches for cancer chemotherapy.
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Affiliation(s)
- HafizMuhammad Imran
- Department of Biochemistry, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.I.); (Y.T.); (S.W.); (X.Y.); (C.L.); (L.G.)
| | - Yixin Tang
- Department of Biochemistry, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.I.); (Y.T.); (S.W.); (X.Y.); (C.L.); (L.G.)
| | - Siyuan Wang
- Department of Biochemistry, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.I.); (Y.T.); (S.W.); (X.Y.); (C.L.); (L.G.)
| | - Xiuzhang Yan
- Department of Biochemistry, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.I.); (Y.T.); (S.W.); (X.Y.); (C.L.); (L.G.)
| | - Chang Liu
- Department of Biochemistry, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.I.); (Y.T.); (S.W.); (X.Y.); (C.L.); (L.G.)
| | - Lei Guo
- Department of Biochemistry, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.I.); (Y.T.); (S.W.); (X.Y.); (C.L.); (L.G.)
| | - Erlei Wang
- College of Food Science and Engineering, Jilin University, Changchun 130062, China
| | - Caina Xu
- Department of Biochemistry, College of Basic Medical Sciences, Jilin University, Changchun 130021, China; (H.I.); (Y.T.); (S.W.); (X.Y.); (C.L.); (L.G.)
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138
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Xiang P, Liyu A, Kwon Y, Hu D, Williams SM, Veličković D, Markillie LM, Chrisler WB, Paša-Tolić L, Zhu Y. Spatial Proteomics toward Subcellular Resolution by Coupling Deep Ultraviolet Laser Ablation with Nanodroplet Sample Preparation. ACS MEASUREMENT SCIENCE AU 2023; 3:459-468. [PMID: 38145026 PMCID: PMC10740121 DOI: 10.1021/acsmeasuresciau.3c00033] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/17/2023] [Accepted: 09/22/2023] [Indexed: 12/26/2023]
Abstract
Multiplexed molecular profiling of tissue microenvironments, or spatial omics, can provide critical insights into cellular functions and disease pathology. The coupling of laser microdissection with mass spectrometry-based proteomics has enabled deep and unbiased mapping of >1000 proteins. However, the throughput of laser microdissection is often limited due to tedious two-step procedures, sequential laser cutting, and sample collection. The two-step procedure also hinders the further improvement of spatial resolution to <10 μm as needed for subcellular proteomics. Herein, we developed a high-throughput and high-resolution spatial proteomics platform by seamlessly coupling deep ultraviolet (DUV) laser ablation (LA) with nanoPOTS (Nanodroplet Processing in One pot for Trace Samples)-based sample preparation. We demonstrated the DUV-LA system can quickly isolate and collect tissue samples at a throughput of ∼30 spots/min and a spatial resolution down to 2 μm from a 10 μm thick human pancreas tissue section. To improve sample recovery, we developed a proximity aerosol collection approach by placing DMSO droplets close to LA spots. We demonstrated the DUV-LA-nanoPOTS platform can detect an average of 1312, 1533, and 1966 proteins from ablation spots with diameters of 7, 13, and 19 μm, respectively. In a proof-of-concept study, we isolated and profiled two distinct subcellular regions of the pancreas tissue revealed by hematoxylin and eosin (H&E) staining. Quantitative proteomics revealed proteins specifically enriched to subcellular compartments.
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Affiliation(s)
- Piliang Xiang
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Andrey Liyu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Yumi Kwon
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Dehong Hu
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Sarah M. Williams
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Dušan Veličković
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Lye Meng Markillie
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - William B. Chrisler
- Biological
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Ljiljana Paša-Tolić
- Environmental
Molecular Sciences Laboratory, Pacific Northwest
National Laboratory, Richland, Washington 99354, United States
| | - Ying Zhu
- Department
of Microchemistry, Proteomics, Lipidomics and Next Generation Sequencing, Genentech, 1 DNA Way, South San Francisco, California 94080, United States
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Krell M, Llera B, Brown ZJ. Circulating Tumor DNA and Management of Colorectal Cancer. Cancers (Basel) 2023; 16:21. [PMID: 38201448 PMCID: PMC10778183 DOI: 10.3390/cancers16010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 12/05/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Although the incidence of colorectal cancer (CRC) has decreased as a result of increased screening and awareness, it still remains a major cause of cancer-related death. Additionally, early detection of CRC recurrence by conventional means such as CT, endoscopy, and CEA has not translated into an improvement in survival. Liquid biopsies, such as the detection circulating tumor DNA (ctDNA), have been investigated as a biomarker for patients with CRC in terms of prognosis and recurrence, as well as their use to guide therapy. In this manuscript, we provide an overview of ctDNA as well as its utility in providing prognostic information, using it to guide therapy, and monitoring for recurrence in patients with CRC. In addition, we discuss the influence the site of disease may have on the ability to detect ctDNA in patients with metastatic CRC.
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Affiliation(s)
| | | | - Zachary J. Brown
- Department of Surgery, Division of Surgical Oncology, NYU Langone Health, NYU Grossman Long Island School of Medicine, Mineola, NY 11501, USA; (M.K.); (B.L.)
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140
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Wrenn ED, Apfelbaum AA, Rudzinski ER, Deng X, Jiang W, Sud S, Van Noord RA, Newman EA, Garcia NM, Miyaki A, Hoglund VJ, Bhise SS, Kanaan SB, Waltner OG, Furlan SN, Lawlor ER. Cancer-Associated Fibroblast-Like Tumor Cells Remodel the Ewing Sarcoma Tumor Microenvironment. Clin Cancer Res 2023; 29:5140-5154. [PMID: 37471463 PMCID: PMC10801911 DOI: 10.1158/1078-0432.ccr-23-1111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 06/07/2023] [Accepted: 07/18/2023] [Indexed: 07/22/2023]
Abstract
PURPOSE Despite limited genetic and histologic heterogeneity, Ewing sarcoma (EwS) tumor cells are transcriptionally heterogeneous and display varying degrees of mesenchymal lineage specification in vitro. In this study, we investigated if and how transcriptional heterogeneity of EwS cells contributes to heterogeneity of tumor phenotypes in vivo. EXPERIMENTAL DESIGN Single-cell proteogenomic-sequencing of EwS cell lines was performed and integrated with patient tumor transcriptomic data. Cell subpopulations were isolated by FACS for assessment of gene expression and phenotype. Digital spatial profiling and human whole transcriptome analysis interrogated transcriptomic heterogeneity in EwS xenografts. Tumor cell subpopulations and matrix protein deposition were evaluated in xenografts and patient tumors using multiplex immunofluorescence staining. RESULTS We identified CD73 as a biomarker of highly mesenchymal EwS cell subpopulations in tumor models and patient biopsies. CD73+ tumor cells displayed distinct transcriptional and phenotypic properties, including selective upregulation of genes that are repressed by EWS::FLI1, and increased migratory potential. CD73+ cells were distinguished in vitro and in vivo by increased expression of matrisomal genes and abundant deposition of extracellular matrix (ECM) proteins. In epithelial-derived malignancies, ECM is largely deposited by cancer-associated fibroblasts (CAF), and we thus labeled CD73+ EwS cells, CAF-like tumor cells. Marked heterogeneity of CD73+ EwS cell frequency and distribution was detected in tumors in situ, and CAF-like tumor cells and associated ECM were observed in peri-necrotic regions and invasive foci. CONCLUSIONS EwS tumor cells can adopt CAF-like properties, and these distinct cell subpopulations contribute to tumor heterogeneity by remodeling the tumor microenvironment. See related commentary by Kuo and Amatruda, p. 5002.
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Affiliation(s)
- Emma D. Wrenn
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - April A. Apfelbaum
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
- Cancer Biology PhD Program, University of Michigan, Ann Arbor, Michigan
| | - Erin R. Rudzinski
- Pathology Department, Seattle Children’s Hospital, Seattle, Washington
| | - Xuemei Deng
- Pathology Department, Seattle Children’s Hospital, Seattle, Washington
| | - Wei Jiang
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Sudha Sud
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | | | - Erika A. Newman
- Rogel Cancer Center, University of Michigan, Ann Arbor, Michigan
| | - Nicolas M. Garcia
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Aya Miyaki
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Virginia J. Hoglund
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
| | - Shruti S. Bhise
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Sami B. Kanaan
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Olivia G. Waltner
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Scott N. Furlan
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, WA
| | - Elizabeth R. Lawlor
- Ben Towne Center for Childhood Cancer Research, Seattle Children’s Research Institute, Seattle, WA
- Clinical Research Division, Fred Hutchinson Cancer Center, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, WA
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141
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Zhu Q, Zhao X, Zhang Y, Li Y, Liu S, Han J, Sun Z, Wang C, Deng D, Wang S, Tang Y, Huang Y, Jiang S, Tian C, Chen X, Yuan Y, Li Z, Yang T, Lai T, Liu Y, Yang W, Zou X, Zhang M, Cui H, Liu C, Jin X, Hu Y, Chen A, Xu X, Li G, Hou Y, Liu L, Liu S, Fang L, Chen W, Wu L. Single cell multi-omics reveal intra-cell-line heterogeneity across human cancer cell lines. Nat Commun 2023; 14:8170. [PMID: 38071219 PMCID: PMC10710513 DOI: 10.1038/s41467-023-43991-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
Human cancer cell lines have long served as tools for cancer research and drug discovery, but the presence and the source of intra-cell-line heterogeneity remain elusive. Here, we perform single-cell RNA-sequencing and ATAC-sequencing on 42 and 39 human cell lines, respectively, to illustrate both transcriptomic and epigenetic heterogeneity within individual cell lines. Our data reveal that transcriptomic heterogeneity is frequently observed in cancer cell lines of different tissue origins, often driven by multiple common transcriptional programs. Copy number variation, as well as epigenetic variation and extrachromosomal DNA distribution all contribute to the detected intra-cell-line heterogeneity. Using hypoxia treatment as an example, we demonstrate that transcriptomic heterogeneity could be reshaped by environmental stress. Overall, our study performs single-cell multi-omics of commonly used human cancer cell lines and offers mechanistic insights into the intra-cell-line heterogeneity and its dynamics, which would serve as an important resource for future cancer cell line-based studies.
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Affiliation(s)
- Qionghua Zhu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Xin Zhao
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yuanhang Zhang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Yanping Li
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Shang Liu
- BGI Research, 518083, Shenzhen, China
| | - Jingxuan Han
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Zhiyuan Sun
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Chunqing Wang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Daqi Deng
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Yisen Tang
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Siyuan Jiang
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Chi Tian
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Xi Chen
- BGI Research, 518083, Shenzhen, China
| | - Yue Yuan
- BGI Research, 518083, Shenzhen, China
| | - Zeyu Li
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | - Tao Yang
- China National GeneBank, 518120, Shenzhen, China
| | - Tingting Lai
- China National GeneBank, 518120, Shenzhen, China
| | - Yiqun Liu
- China National GeneBank, 518120, Shenzhen, China
| | - Wenzhen Yang
- China National GeneBank, 518120, Shenzhen, China
| | - Xuanxuan Zou
- BGI Research, 518083, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, 100049, Beijing, China
| | | | - Huanhuan Cui
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China
| | | | - Xin Jin
- BGI Research, 518083, Shenzhen, China
| | - Yuhui Hu
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Ao Chen
- BGI Research, 518083, Shenzhen, China
- JFL-BGI STOmics Center, Jinfeng Laboratory, 401329, Chongqing, China
- The Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong, China
| | - Xun Xu
- BGI Research, 518083, Shenzhen, China
| | - Guipeng Li
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China
| | - Yong Hou
- BGI Research, 518083, Shenzhen, China
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, 518100, Shenzhen, China
| | - Longqi Liu
- BGI Research, 518083, Shenzhen, China.
- BGI Research, 310012, Hangzhou, China.
- Shenzhen Bay Laboratory, 518000, Shenzhen, China.
| | - Shiping Liu
- BGI Research, 518083, Shenzhen, China.
- The Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong, China.
- Shenzhen Key Laboratory of Single-Cell Omics, BGI-Shenzhen, 518100, Shenzhen, China.
- BGI Research, 310012, Hangzhou, China.
- Shenzhen Bay Laboratory, 518000, Shenzhen, China.
| | - Liang Fang
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Academy for Advanced Interdisciplinary Studies, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Wei Chen
- Shenzhen Key Laboratory of Gene Regulation and Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
- Department of Systems Biology, School of Life Sciences, Southern University of Science and Technology, 518055, Shenzhen, China.
| | - Liang Wu
- BGI Research, 518083, Shenzhen, China.
- JFL-BGI STOmics Center, Jinfeng Laboratory, 401329, Chongqing, China.
- BGI Research, 401329, Chongqing, China.
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142
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Olejarz W, Basak G. Emerging Therapeutic Targets and Drug Resistance Mechanisms in Immunotherapy of Hematological Malignancies. Cancers (Basel) 2023; 15:5765. [PMID: 38136311 PMCID: PMC10741639 DOI: 10.3390/cancers15245765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 12/06/2023] [Indexed: 12/24/2023] Open
Abstract
CAR-T cell therapy has revolutionized the treatment of hematological malignancies with high remission rates in the case of ALL and NHL. This therapy has some limitations such as long manufacturing periods, persistent restricted cell sources and high costs. Moreover, combination regimens increase the risk of immune-related adverse events, so the identification new therapeutic targets is important to minimize the risk of toxicities and to guide more effective approaches. Cancer cells employ several mechanisms to evade immunosurveillance, which causes resistance to immunotherapy; therefore, a very important therapeutic approach is to focus on the development of rational combinations of targeted therapies with non-overlapping toxicities. Recent progress in the development of new inhibitory clusters of differentiation (CDs), signaling pathway molecules, checkpoint inhibitors, and immunosuppressive cell subsets and factors in the tumor microenvironment (TME) has significantly improved anticancer responses. Novel strategies regarding combination immunotherapies with CAR-T cells are the most promising approach to cure cancer.
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Affiliation(s)
- Wioletta Olejarz
- Department of Biochemistry and Pharmacogenomics, Faculty of Pharmacy, Medical University of Warsaw, 02-091 Warsaw, Poland
- Centre for Preclinical Research, Medical University of Warsaw, 02-091 Warsaw, Poland
| | - Grzegorz Basak
- Department of Hematology, Transplantation and Internal Medicine, Medical University of Warsaw, 02-091 Warsaw, Poland;
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143
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Wan Y, Mu Q, Krzysztoń R, Cohen J, Coraci D, Helenek C, Tompkins C, Lin A, Farquhar K, Cross E, Wang J, Balázsi G. Adaptive DNA amplification of synthetic gene circuit opens a way to overcome cancer chemoresistance. Proc Natl Acad Sci U S A 2023; 120:e2303114120. [PMID: 38019857 DOI: 10.1073/pnas.2303114120] [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: 02/22/2023] [Accepted: 09/27/2023] [Indexed: 12/01/2023] Open
Abstract
Drug resistance continues to impede the success of cancer treatments, creating a need for experimental model systems that are broad, yet simple, to allow the identification of mechanisms and novel countermeasures applicable to many cancer types. To address these needs, we investigated a set of engineered mammalian cell lines with synthetic gene circuits integrated into their genome that evolved resistance to Puromycin. We identified DNA amplification as the mechanism underlying drug resistance in 4 out of 6 replicate populations. Triplex-forming oligonucleotide (TFO) treatment combined with Puromycin could efficiently suppress the growth of cell populations with DNA amplification. Similar observations in human cancer cell lines suggest that TFOs could be broadly applicable to mitigate drug resistance, one of the major difficulties in treating cancer.
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Affiliation(s)
- Yiming Wan
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Quanhua Mu
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong Special Administrative Region 999077, China
| | - Rafał Krzysztoń
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Joseph Cohen
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Damiano Coraci
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Christopher Helenek
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | | | - Annie Lin
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | - Kevin Farquhar
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
| | | | - Jiguang Wang
- Department of Chemical and Biological Engineering, Division of Life Science, State Key Laboratory of Molecular Neuroscience, The Hong Kong University of Science and Technology, Hong Kong Special Administrative Region 999077, China
| | - Gábor Balázsi
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY 11794
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY 11794
- Stony Brook Cancer Center, Stony Brook University, Stony Brook, NY 11794
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144
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Schenkel JM, Pauken KE. Localization, tissue biology and T cell state - implications for cancer immunotherapy. Nat Rev Immunol 2023; 23:807-823. [PMID: 37253877 DOI: 10.1038/s41577-023-00884-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/26/2023] [Indexed: 06/01/2023]
Abstract
Tissue localization is a critical determinant of T cell immunity. CD8+ T cells are contact-dependent killers, which requires them to physically be within the tissue of interest to kill peptide-MHC class I-bearing target cells. Following their migration and extravasation into tissues, T cells receive many extrinsic cues from the local microenvironment, and these signals shape T cell differentiation, fate and function. Because major organ systems are variable in their functions and compositions, they apply disparate pressures on T cells to adapt to the local microenvironment. Additional complexity arises in the context of malignant lesions (either primary or metastatic), and this has made understanding the factors that dictate T cell function and longevity in tumours challenging. Moreover, T cell differentiation state influences how cues from the microenvironment are interpreted by tissue-infiltrating T cells, highlighting the importance of T cell state in the context of tissue biology. Here, we review the intertwined nature of T cell differentiation state, location, survival and function, and explain how dysfunctional T cell populations can adopt features of tissue-resident memory T cells to persist in tumours. Finally, we discuss how these factors have shaped responses to cancer immunotherapy.
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Affiliation(s)
- Jason M Schenkel
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- Department of Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Kristen E Pauken
- Department of Immunology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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145
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Ritu, Chandra P, Das A. Immune checkpoint targeting antibodies hold promise for combinatorial cancer therapeutics. Clin Exp Med 2023; 23:4297-4322. [PMID: 37804358 DOI: 10.1007/s10238-023-01201-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Accepted: 09/19/2023] [Indexed: 10/09/2023]
Abstract
Through improving the immune system's ability to recognize and combat tumor cells as well as its receptivity to changes in the tumor microenvironment, immunotherapy has emerged as a highly successful addition to the treatment of cancer. However, tumor heterogeneity poses a significant challenge in cancer therapy as it can undermine the anti-tumor immune response through the manipulation of the extracellular matrix. To address these challenges and improve targeted therapies and combination treatments, the food and drug administration has approved several immunomodulatory antibodies to suppress immunological checkpoints. Combinatorial therapies necessitate the identification of multiple targets that regulate the intricate communication between immune cells, cytokines, chemokines, and cellular responses within the tumor microenvironment. The purpose of this study is to provide a comprehensive overview of the ongoing clinical trials involving immunomodulatory antibodies in various cancer types. It explores the potential of these antibodies to modulate the immune system and enhance anti-tumor responses. Additionally, it discusses the perspectives and prospects of immunomodulatory therapeutics in cancer treatment. Although immunotherapy shows great promise in cancer treatment, it is not exempt from side effects that can arise due to hyperactivity of the immune system. Therefore, understanding the intricate balance between immune activation and regulation is crucial for minimizing these adverse effects and optimizing treatment outcomes. This study aims to contribute to the growing body of knowledge surrounding immunomodulatory antibodies and their potential as effective therapeutic options in cancer treatment, ultimately paving the way for improved patient outcomes and deepening our perception of the intricate interactivity between the immune system and tumors.
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Affiliation(s)
- Ritu
- Department of Biotechnology, Delhi Technological University, Main Bawana Road, New Delhi, 110042, India
| | - Prakash Chandra
- Department of Biotechnology, Delhi Technological University, Main Bawana Road, New Delhi, 110042, India
| | - Asmita Das
- Department of Biotechnology, Delhi Technological University, Main Bawana Road, New Delhi, 110042, India.
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146
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Abbas E, Fanni SC, Bandini C, Francischello R, Febi M, Aghakhanyan G, Ambrosini I, Faggioni L, Cioni D, Lencioni RA, Neri E. Delta-radiomics in cancer immunotherapy response prediction: A systematic review. Eur J Radiol Open 2023; 11:100511. [PMID: 37520768 PMCID: PMC10371799 DOI: 10.1016/j.ejro.2023.100511] [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: 05/10/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023] Open
Abstract
Background The new immunotherapies have not only changed the oncological therapeutic approach but have also made it necessary to develop new imaging methods for assessing the response to treatment. Delta radiomics consists of the analysis of radiomic features variation between different medical images, usually before and after therapy. Purpose This review aims to evaluate the role of delta radiomics in the immunotherapy response assessment. Methods A systematic search was performed in PubMed, Scopus, and Web Of Science using "delta radiomics AND immunotherapy" as search terms. The included articles' methodological quality was measured using the Radiomics Quality Score (RQS) tool. Results Thirteen articles were finally included in the systematic review. Overall, the RQS of the included studies ranged from 4 to 17, with a mean RQS total of 11,15 ± 4,18 with a corresponding percentage of 30.98 ± 11.61 %. Eleven articles out of 13 performed imaging at multiple time points. All the included articles performed feature reduction. No study carried out prospective validation, decision curve analysis, or cost-effectiveness analysis. Conclusions Delta radiomics has been demonstrated useful in evaluating the response in oncologic patients undergoing immunotherapy. The overall quality was found law, due to the lack of prospective design and external validation. Thus, further efforts are needed to bring delta radiomics a step closer to clinical implementation.
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Affiliation(s)
- Engy Abbas
- The Joint Department of Medical Imaging, University of Toronto, University Health Network, Sinai Health System, Women’s College Hospital, 610 University Ave, Toronto, ON, Canada M5G 2M9
| | | | - Claudio Bandini
- Department of Translational Research, Academic Radiology, University of Pisa, Pisa, Italy
| | - Roberto Francischello
- Department of Translational Research, Academic Radiology, University of Pisa, Pisa, Italy
| | - Maria Febi
- Department of Translational Research, Academic Radiology, University of Pisa, Pisa, Italy
| | - Gayane Aghakhanyan
- Department of Translational Research, Academic Radiology, University of Pisa, Pisa, Italy
| | - Ilaria Ambrosini
- Department of Translational Research, Academic Radiology, University of Pisa, Pisa, Italy
| | - Lorenzo Faggioni
- Department of Translational Research, Academic Radiology, University of Pisa, Pisa, Italy
| | - Dania Cioni
- Department of Translational Research, Academic Radiology, University of Pisa, Pisa, Italy
| | | | - Emanuele Neri
- The Joint Department of Medical Imaging, University of Toronto, University Health Network, Sinai Health System, Women’s College Hospital, 610 University Ave, Toronto, ON, Canada M5G 2M9
- Department of Translational Research, Academic Radiology, University of Pisa, Pisa, Italy
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147
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Zhang L, Bass HW, Irianto J, Mallory X. Integrating SNVs and CNAs on a phylogenetic tree from single-cell DNA sequencing data. Genome Res 2023; 33:2002-2017. [PMID: 37993137 PMCID: PMC10760445 DOI: 10.1101/gr.277249.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/25/2023] [Indexed: 11/24/2023]
Abstract
Single-cell DNA sequencing enables the construction of evolutionary trees that can reveal how tumors gain mutations and grow. Different whole-genome amplification procedures render genomic materials of different characteristics, often suitable for the detection of either single-nucleotide variation or copy number aberration, but not ideally for both. Consequently, this hinders the inference of a comprehensive phylogenetic tree and limits opportunities to investigate the interplay of SNVs and CNAs. Existing methods such as SCARLET and COMPASS require that the SNVs and CNAs are detected from the same sets of cells, which is technically challenging. Here we present a novel computational tool, SCsnvcna, that places SNVs on a tree inferred from CNA signals, whereas the sets of cells rendering the SNVs and CNAs are independent, offering a more practical solution in terms of the technical challenges. SCsnvcna is a Bayesian probabilistic model using both the genotype constraints on the tree and the cellular prevalence to search the optimal solution. Comprehensive simulations and comparison with seven state-of-the-art methods show that SCsnvcna is robust and accurate in a variety of circumstances. Particularly, SCsnvcna most frequently produces the lowest error rates, with ability to scale to a wide range of numerical values for leaf nodes in the tree, SNVs, and SNV cells. The application of SCsnvcna to two published colorectal cancer data sets shows highly consistent placement of SNV cells and SNVs with the original study while also supporting a refined placement of ATP7B, illustrating SCsnvcna's value in analyzing complex multitumor samples.
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Affiliation(s)
- Liting Zhang
- Department of Computer Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Hank W Bass
- Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA
| | - Jerome Irianto
- College of Medicine, Florida State University, Tallahassee, Florida 32306, USA
| | - Xian Mallory
- Department of Computer Science, Florida State University, Tallahassee, Florida 32306, USA;
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148
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Dhiman A, Kothary V, Witmer HDD, Bregio C, Sood D, Ong CT, Polite B, Eng OS, Shergill A, Turaga KK. Role of Tumor-informed Personalized Circulating Tumor DNA Assay in Informing Recurrence in Patients With Peritoneal Metastases From Colorectal and High-grade Appendix Cancer Undergoing Curative-intent Surgery. Ann Surg 2023; 278:925-931. [PMID: 36994703 DOI: 10.1097/sla.0000000000005856] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
OBJECTIVE To investigate the role of a personalized, tumor-informed circulating tumor DNA (ctDNA) assay in informing recurrence in patients with peritoneal metastases (PM) from colorectal (CRC) and high-grade appendix (HGA) cancer after curative cytoreductive surgery with hyperthermic intraperitoneal chemotherapy (CRS-HIPEC). BACKGROUND Over 50% of patients with CRC/HGA-PM recur after optimal CRS-HIPEC. The limited sensitivity of axial imaging and diagnostic biomarkers is a significant cause of delay in the detection of recurrence and initiation of further therapies. Plasma ctDNA has a promising role in monitoring response to treatment and/or recurrence after primary cancer resection. METHODS Patients with CRC/HGA-PM who underwent curative CRS-HIPEC and serial postresection ctDNA assessments were included. Patients with rising postoperative ctDNA levels were compared with those with stable, undetectable ctDNA levels. Primary outcomes were the percentage of patients with recurrence and disease-free survival (DFS). Secondary outcomes were overall survival, ctDNA sensitivity, lead time, and performance of ctDNA compared with carcinoembryonic antigen. RESULTS One hundred thirty serial postresection ctDNA assessments [median 4, interquartile range (IQR), 3 to 5] were performed in 33 patients (n = 13 CRC, n = 20 HGA) who underwent completeness of cytoreduction-0/1 CRS with a median follow-up of 13 months. Of the 19 patients with rising ctDNA levels, 90% recurred versus 21% in the stable ctDNA group (n = 14, < 0.001). Median DFS in the rising ctDNA cohort was 11 months (IQR, 6 to 12) and not reached in the stable ( P = 0.01). A rising ctDNA level was the most significant factor associated with DFS (hazard ratio: 3.67, 95% CI: 1.06-12.66, P = 0.03). The sensitivity and specificity of rising ctDNA levels in predicting recurrence were 85% and 84.6%, respectively. The median ctDNA lead time was 3 months (IQR, 1 to 4). Carcinoembryonic antigen was less sensitive (50%) than ctDNA. CONCLUSIONS This study supports the clinical validity of serial ctDNA assessment as a strong prognostic biomarker in informing recurrence in patients with CRC/HGA-PM undergoing curative resection. It also holds promises for informing future clinical trial designs and further research.
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Affiliation(s)
- Ankit Dhiman
- Department of Surgery, Section of General Surgery and Surgical Oncology, University of Chicago Medical Center, Chicago, IL
| | - Vishesh Kothary
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center, Chicago, IL
| | - Hunter D D Witmer
- Department of Surgery, Section of General Surgery and Surgical Oncology, University of Chicago Medical Center, Chicago, IL
| | - Celyn Bregio
- Pritzker School of Medicine, University of Chicago, Chicago, IL
| | - Divya Sood
- Department of Surgery, Section of General Surgery and Surgical Oncology, University of Chicago Medical Center, Chicago, IL
| | - Cecilia T Ong
- Department of Surgery, Section of General Surgery and Surgical Oncology, University of Chicago Medical Center, Chicago, IL
| | - Blase Polite
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center, Chicago, IL
| | - Oliver S Eng
- Division of Surgical Oncology, Department of Surgery, University of California, Irvine, Orange, CA
| | - Ardaman Shergill
- Department of Medicine, Section of Hematology/Oncology, University of Chicago Medical Center, Chicago, IL
| | - Kiran K Turaga
- Department of Surgery, Section of General Surgery and Surgical Oncology, University of Chicago Medical Center, Chicago, IL
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149
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Hyug Choi J, Sook Jun M, Yong Jeon J, Kim HS, Kyung Kim Y, Ho Jeon C, Hwan Choi S, Sun Kim D, Han MH, Won Oh J. Global lineage evolution pattern of sars-cov-2 in Africa, America, Europe, and Asia: A comparative analysis of variant clusters and their relevance across continents. J Transl Int Med 2023; 11:410-422. [PMID: 38130632 PMCID: PMC10732492 DOI: 10.2478/jtim-2023-0118] [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] [Indexed: 12/23/2023] Open
Abstract
Objective The objective of this study is to provide a comparative analysis of variant clusters and their relevance across Africa, America, Europe, and Asia, in order to understand the evolutionary patterns of the virus across different regions and to inform the development of targeted interventions and genomic surveillance eforts. Methods The study analyzed the global lineage evolution pattern of 74, 075 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes from 32 countries across four continents, focusing on variant clusters and their relevance across regions. Variants were weighted according to their hierarchical level. The correlation between variants was visualized through Dimensionality reduction analysis and Pairwise Pearson's correlation. We presented a reconstructed phylogenetic tree based on correlation analysis and variant weights. Results The analysis revealed that each continent had distinct variant clusters and different evolutionary patterns. The Americas had two clustered variants before lineage divergence and a downstream confluence lineage, Europe had bifurcation into two global lineages with an early occurrence of certain cluster while Asia had a downstream confluence of two large lineages diverging by two distinct clusters. Based on the cluster patterns of shared variants of the SARS-CoV-2 virus, Africa demonstrated a relatively clear distinction among three distinct regions. Conclusions The study provides insights into the evolutionary patterns of SARS-CoV-2 and highlights the importance of international collaboration in tracking and responding to emerging variants. The study found that the global pandemic was driven by Omicron variants that evolved with significant differences between countries and regions, and with different patterns across continents.
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Affiliation(s)
- June Hyug Choi
- Department of Anatomy, BK21 FOUR KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Mee Sook Jun
- Department of Internal Medicine, Chungbuk National University, Cheongju, Yonsei University-Industry Foundation, Seoul, Republic of Korea
| | | | - Hae-Suk Kim
- Theragen Bio Co., Ltd., Seongnam-si, Republic of Korea
| | - Yu Kyung Kim
- Department of Clinical Pathology, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Chang Ho Jeon
- Department of Laboratory Medicine, Catholic University of Daegu School of Medicine, Daegu, Republic of Korea
| | - Seock Hwan Choi
- Department of Urology, School of Medicine, BioMedical Research Institute, Kyungpook National University Hospital, Kyungpook National University, Daegu, Republic of Korea
| | - Dong Sun Kim
- Department of Anatomy, BK21 FOUR KNU Convergence Educational Program of Biomedical Sciences for Creative Future Talents, School of Medicine, Kyungpook National University, Daegu, Republic of Korea
| | - Man-Hoon Han
- Department of Pathology, School of Medicine, BioMedical Research Institute, Kyungpook National University Hospital, Kyungpook National University, Daegu, Republic of Korea
| | - Ji Won Oh
- Department of Anatomy, Brain Korea 21 PLUS Project for Medical Science, Yonsei University College of Medicine, Seoul, Republic of Korea
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150
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Carrasco R, Ingelmo-Torres M, Oriola J, Roldán FL, Rodríguez-Carunchio L, Herranz S, Mellado B, Alcaraz A, Izquierdo L, Mengual L. Assessment of aggressive bladder cancer mutations in plasma cell-free DNA. Front Oncol 2023; 13:1270962. [PMID: 38098507 PMCID: PMC10720633 DOI: 10.3389/fonc.2023.1270962] [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: 08/01/2023] [Accepted: 11/13/2023] [Indexed: 12/17/2023] Open
Abstract
Background and aims The spatial and temporal genetic heterogeneity of bladder cancer (BC) makes challenging to find specific drivers of metastatic disease, thus preventing to determine those BC patients at high risk of tumor progression. Our aim was to identify DNA mutations providing aggressive behavior to bladder tumors and analyze them in patients' cell-free DNA (cfDNA) during their follow-up after radical cystectomy (RC) in order to monitor tumor evolution. Methods Six BC patients who underwent RC and presented disease progression during their follow-up were included. Next-generation sequencing was used to determine somatic mutations in several primary tumor and metastatic specimens from each patient. Shared DNA mutations between primary bladder tumor and metastatic sites were identified in cfDNA samples through droplet digital PCR. Results Besides BC genetic heterogeneity, specific mutations in at least one of these genes -TERT, ATM, RB1, and FGFR3- were found in primary tumors and their metastases in all patients. These mutations were also identified in the patients' cfDNA at different follow-up time points. Additionally, the dynamic changes of these mutations in cfDNA allowed us to determine tumor evolution in response to treatment. Conclusion The analysis of BC mutations associated with poor prognosis in plasma cfDNA could be a valuable tool to monitor tumor evolution, thus improving the clinical management of BC patients.
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Affiliation(s)
- Raquel Carrasco
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, Barcelona, Spain
- Genètica i tumors urològics, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain
| | - Mercedes Ingelmo-Torres
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, Barcelona, Spain
- Genètica i tumors urològics, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | - Josep Oriola
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain
| | - Fiorella L. Roldán
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, Barcelona, Spain
- Genètica i tumors urològics, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | | | - Sandra Herranz
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Begoña Mellado
- Servei d’Oncologia Mèdica, Hospital Clínic de Barcelona, Barcelona, Spain
| | - Antonio Alcaraz
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, Barcelona, Spain
- Genètica i tumors urològics, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | - Laura Izquierdo
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, Barcelona, Spain
- Genètica i tumors urològics, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
| | - Lourdes Mengual
- Laboratori i Servei d’Urologia, Hospital Clínic de Barcelona, Barcelona, Spain
- Genètica i tumors urològics, Fundació de Recerca Clínic Barcelona-Institut d’Investigacions Biomèdiques August Pi i Sunyer (FRCB-IDIBAPS), Barcelona, Spain
- Departament de Biomedicina, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain
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