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Ali A, Manzoor S, Ali T, Asim M, Muhammad G, Ahmad A, Jamaludin MI, Devaraj S, Munawar N. Innovative aspects and applications of single cell technology for different diseases. Am J Cancer Res 2024; 14:4028-4048. [PMID: 39267684 PMCID: PMC11387862 DOI: 10.62347/vufu1836] [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: 06/21/2024] [Accepted: 08/24/2024] [Indexed: 09/15/2024] Open
Abstract
Recent developments in single-cell technologies have provided valuable insights from cancer genomics to complex microbial communities. Single-cell technologies including the RNA-seq, next-generation sequencing (NGS), epigenomics, genomics, and transcriptomics can be used to uncover the single cell nature and molecular characterization of individual cells. These technologies also reveal the cellular transition states, evolutionary relationships between genes, the complex structure of single-cell populations, cell-to-cell interaction leading to biological discoveries and more reliable than traditional bulk technologies. These technologies are becoming the first choice for the early detection of inflammatory biomarkers affecting the proliferation and progression of tumor cells in the tumor microenvironment and improving the clinical efficacy of patients undergoing immunotherapy. These technologies also hold a central position in the detection of checkpoint inhibitors and thus determining the signaling pathways evoked by tumor invasion. This review addressed the emerging approaches of single cell-based technologies in cancer immunotherapies and different human diseases at cellular and molecular levels and the emerging role of sequencing technologies leading to drug discovery. Advancements in these technologies paved for discovering novel diagnostic markers for better understanding the pathological and biochemical mechanisms also for controlling the rate of different diseases.
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Affiliation(s)
- Ashiq Ali
- Department of Histology and Embryology, Shantou University Medical College Shantou 515041, Guangdong, China
| | - Saba Manzoor
- Department of Zoology, University of Sialkot Sialkot 51310, Pakistan
| | - Tayyab Ali
- Clinico-Molecular Biochemistry Laboratory, Department of Biochemistry, University of Agriculture Faisalabad 38000, Pakistan
| | - Muhammad Asim
- Clinico-Molecular Biochemistry Laboratory, Department of Biochemistry, University of Agriculture Faisalabad 38000, Pakistan
| | - Ghulam Muhammad
- Jinnah Burn and Reconstructive Surgery Centre, Jinnah Hospital, Allama Iqbal Medical College Lahore 54000, Pakistan
| | - Aftab Ahmad
- Biochemistry/Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture Faisalabad 38040, Pakistan
| | - Mohamad Ikhwan Jamaludin
- BioInspired Device and Tissue Engineering Research Group (BioInspira), Department of Biomedical Engineering and Health Sciences, Faculty of Electrical Engineering, Universiti Teknologi Malaysia Johor Bahru 81310, Johor, Malaysia
| | - Sutha Devaraj
- Graduate School of Medicine, Perdana University Wisma Chase Perdana, Changkat Semantan, Damansara Heights, Kuala Lumpur 50490, Malaysia
| | - Nayla Munawar
- Department of Chemistry, College of Science, United Arab Emirates University Al-Ain 15551, United Arab Emirates
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Orrapin S, Thongkumkoon P, Udomruk S, Moonmuang S, Sutthitthasakul S, Yongpitakwattana P, Pruksakorn D, Chaiyawat P. Deciphering the Biology of Circulating Tumor Cells through Single-Cell RNA Sequencing: Implications for Precision Medicine in Cancer. Int J Mol Sci 2023; 24:12337. [PMID: 37569711 PMCID: PMC10418766 DOI: 10.3390/ijms241512337] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/25/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
Circulating tumor cells (CTCs) hold unique biological characteristics that directly involve them in hematogenous dissemination. Studying CTCs systematically is technically challenging due to their extreme rarity and heterogeneity and the lack of specific markers to specify metastasis-initiating CTCs. With cutting-edge technology, single-cell RNA sequencing (scRNA-seq) provides insights into the biology of metastatic processes driven by CTCs. Transcriptomics analysis of single CTCs can decipher tumor heterogeneity and phenotypic plasticity for exploring promising novel therapeutic targets. The integrated approach provides a perspective on the mechanisms underlying tumor development and interrogates CTCs interactions with other blood cell types, particularly those of the immune system. This review aims to comprehensively describe the current study on CTC transcriptomic analysis through scRNA-seq technology. We emphasize the workflow for scRNA-seq analysis of CTCs, including enrichment, single cell isolation, and bioinformatic tools applied for this purpose. Furthermore, we elucidated the translational knowledge from the transcriptomic profile of individual CTCs and the biology of cancer metastasis for developing effective therapeutics through targeting key pathways in CTCs.
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Affiliation(s)
- Santhasiri Orrapin
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Patcharawadee Thongkumkoon
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Sasimol Udomruk
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
- Musculoskeletal Science and Translational Research (MSTR) Center, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
| | - Sutpirat Moonmuang
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Songphon Sutthitthasakul
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Petlada Yongpitakwattana
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
| | - Dumnoensun Pruksakorn
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
- Musculoskeletal Science and Translational Research (MSTR) Center, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
- Department of Orthopedics, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
| | - Parunya Chaiyawat
- Center of Multidisciplinary Technology for Advanced Medicine (CMUTEAM), Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand; (S.O.); (P.T.); (S.U.); (S.M.); (S.S.); (P.Y.); (D.P.)
- Musculoskeletal Science and Translational Research (MSTR) Center, Faculty of Medicine, Chiang Mai University, Muang, Chiang Mai 50200, Thailand
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Koelsch N, Manjili MH. From Reductionistic Approach to Systems Immunology Approach for the Understanding of Tumor Microenvironment. Int J Mol Sci 2023; 24:12086. [PMID: 37569461 PMCID: PMC10419122 DOI: 10.3390/ijms241512086] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Revised: 07/23/2023] [Accepted: 07/27/2023] [Indexed: 08/13/2023] Open
Abstract
The tumor microenvironment (TME) is a complex and dynamic ecosystem that includes a variety of immune cells mutually interacting with tumor cells, structural/stromal cells, and each other. The immune cells in the TME can have dual functions as pro-tumorigenic and anti-tumorigenic. To understand such paradoxical functions, the reductionistic approach classifies the immune cells into pro- and anti-tumor cells and suggests the therapeutic blockade of the pro-tumor and induction of the anti-tumor immune cells. This strategy has proven to be partially effective in prolonging patients' survival only in a fraction of patients without offering a cancer cure. Recent advances in multi-omics allow taking systems immunology approach. This essay discusses how a systems immunology approach could revolutionize our understanding of the TME by suggesting that internetwork interactions of the immune cell types create distinct collective functions independent of the function of each cellular constituent. Such collective function can be understood by the discovery of the immunological patterns in the TME and may be modulated as a therapeutic means for immunotherapy of cancer.
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Affiliation(s)
- Nicholas Koelsch
- Department of Microbiology & Immunology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA;
| | - Masoud H. Manjili
- Department of Microbiology & Immunology, Virginia Commonwealth University School of Medicine, Richmond, VA 23298, USA;
- VCU Massey Cancer Center, 401 College Street, Boc 980035, Richmond, VA 23298, USA
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Lawrence R, Watters M, Davies CR, Pantel K, Lu YJ. Circulating tumour cells for early detection of clinically relevant cancer. Nat Rev Clin Oncol 2023:10.1038/s41571-023-00781-y. [PMID: 37268719 DOI: 10.1038/s41571-023-00781-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 63.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 06/04/2023]
Abstract
Given that cancer mortality is usually a result of late diagnosis, efforts in the field of early detection are paramount to reducing cancer-related deaths and improving patient outcomes. Increasing evidence indicates that metastasis is an early event in patients with aggressive cancers, often occurring even before primary lesions are clinically detectable. Metastases are usually formed from cancer cells that spread to distant non-malignant tissues via the blood circulation, termed circulating tumour cells (CTCs). CTCs have been detected in patients with early stage cancers and, owing to their association with metastasis, might indicate the presence of aggressive disease, thus providing a possible means to expedite diagnosis and treatment initiation for such patients while avoiding overdiagnosis and overtreatment of those with slow-growing, indolent tumours. The utility of CTCs as an early diagnostic tool has been investigated, although further improvements in the efficiency of CTC detection are required. In this Perspective, we discuss the clinical significance of early haematogenous dissemination of cancer cells, the potential of CTCs to facilitate early detection of clinically relevant cancers, and the technological advances that might improve CTC capture and, thus, diagnostic performance in this setting.
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Affiliation(s)
- Rachel Lawrence
- Centre for Biomarkers and Therapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Melissa Watters
- Barts and London School of Medicine and Dentistry, Queen Mary University London, London, UK
| | - Caitlin R Davies
- Centre for Biomarkers and Therapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK
| | - Klaus Pantel
- Department of Tumour Biology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - Yong-Jie Lu
- Centre for Biomarkers and Therapeutics, Barts Cancer Institute, Queen Mary University of London, London, UK.
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Menyailo ME, Zainullina VR, Khozyainova AA, Tashireva LA, Zolotareva SY, Gerashchenko TS, Alifanov VV, Savelieva OE, Grigoryeva ES, Tarabanovskaya NA, Popova NO, Choinzonov EL, Cherdyntseva NV, Perelmuter VM, Denisov EV. Heterogeneity of Circulating Epithelial Cells in Breast Cancer at Single-Cell Resolution: Identifying Tumor and Hybrid Cells. Adv Biol (Weinh) 2023; 7:e2200206. [PMID: 36449636 DOI: 10.1002/adbi.202200206] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 11/13/2022] [Indexed: 12/03/2022]
Abstract
Circulating tumor cells and hybrid cells formed by the fusion of tumor cells with normal cells are leading players in metastasis and have prognostic relevance. This study applies single-cell RNA sequencing to profile CD45-negative and CD45-positive circulating epithelial cells (CECs) in nonmetastatic breast cancer patients. CECs are represented by transcriptionally-distinct populations that include both aneuploid and diploid cells. CD45- CECs are predominantly aneuploid, but one population contained more diploid than aneuploid cells. CD45+ CECs mostly diploid: only two populations have aneuploid cells. Diploid CD45+ CECs annotated as different immune cells, surprisingly harbored many copy number aberrations, and positively correlated to tumor grade. It is noteworthy that cancer-associated signaling pathways areabundant only in one aneuploid CD45- CEC population, which may represent an aggressive subset of circulating tumor cells. Thus, CD45- and CD45+ CECs are highly heterogeneous in breast cancer patients and include aneuploid cells, which are most likely circulating tumor and hybrid cells, respectively, and diploid cells. DNA ploidy analysis can be an effective instrument for identifying tumor and hybrid cells among CECs. Further follow-up study is needed to determine which subsets of circulating tumor and hybrid cells contribute to breast cancer metastasis.
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Affiliation(s)
- Maxim E Menyailo
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Viktoria R Zainullina
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Anna A Khozyainova
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Liubov A Tashireva
- Department of General and Molecular Pathology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Sofia Yu Zolotareva
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Tatiana S Gerashchenko
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Vladimir V Alifanov
- Department of General and Molecular Pathology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Olga E Savelieva
- Department of General and Molecular Pathology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Evgeniya S Grigoryeva
- Laboratory of Molecular Oncology and Immunology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Nataliya A Tarabanovskaya
- Department of General Oncology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Nataliya O Popova
- Department of Chemotherapy, Cancer Research Institute, Tomsk National Research Medical Center Russian Academy of Sciences, Tomsk, Russia
| | - Evgeny L Choinzonov
- Department of Head and Neck Cancer, Cancer Research Institute, Tomsk National Research Medical Center Russian Academy of Sciences, Tomsk, Russia
| | - Nadezhda V Cherdyntseva
- Laboratory of Molecular Oncology and Immunology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Vladimir M Perelmuter
- Department of General and Molecular Pathology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
| | - Evgeny V Denisov
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Russian Academy of Sciences, Tomsk, Russia
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Guo L, Kong D, Liu J, Zhan L, Luo L, Zheng W, Zheng Q, Chen C, Sun S. Breast cancer heterogeneity and its implication in personalized precision therapy. Exp Hematol Oncol 2023; 12:3. [PMID: 36624542 PMCID: PMC9830930 DOI: 10.1186/s40164-022-00363-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/29/2022] [Indexed: 01/11/2023] Open
Abstract
Breast cancer heterogeneity determines cancer progression, treatment effects, and prognosis. However, the precise mechanism for this heterogeneity remains unknown owing to its complexity. Here, we summarize the origins of breast cancer heterogeneity and its influence on disease progression, recurrence, and therapeutic resistance. We review the possible mechanisms of heterogeneity and the research methods used to analyze it. We also highlight the importance of cell interactions for the origins of breast cancer heterogeneity, which can be further categorized into cooperative and competitive interactions. Finally, we provide new insights into precise individual treatments based on heterogeneity.
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Affiliation(s)
- Liantao Guo
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Deguang Kong
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Jianhua Liu
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Ling Zhan
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Lan Luo
- Department of Breast Surgery, The Affiliated Hospital of Guizhou Medical University, No. 28 Guiyi Road, Yunyan District, Guiyang, 550001, Guizhou, China
| | - Weijie Zheng
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Qingyuan Zheng
- Department of Urology, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China
| | - Chuang Chen
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China.
| | - Shengrong Sun
- Department of Breast and Thyroid Surgery, Renmin Hospital of Wuhan University, No. 238 Jiefang Road, Wuchang District, Wuhan, 430060, Hubei, China.
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Pang S, Xu S, Wang L, Wu H, Chu Y, Ma X, Li Y, Zou B, Wang S, Zhou G. Molecular profiles of single circulating tumor cells from early breast cancer patients with different lymph node statuses. Thorac Cancer 2022; 14:156-167. [PMID: 36408679 PMCID: PMC9834698 DOI: 10.1111/1759-7714.14728] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 11/22/2022] Open
Abstract
BACKGROUND Characterization of early breast cancer circulating tumor cells (CTCs) may provide valuable information on tumor metastasis. METHODS We used immunomagnetic nanospheres to capture CTCs from the peripheral blood of eight early breast cancer patients and then performed single-cell RNA sequencing using our proposed bead-dd-seq method. RESULTS CTCs displayed obvious tumor cell characteristics, such as the activation of oxidative stress, proliferation, and promotion of metastasis. CTCs were clustered into two subtypes significantly correlated with the lymph node metastasis status of patients. CTCs in subtype 1 showed a strong metastatic ability because these CTCs have the phenotype of partial epithelial-mesenchymal transition and enriched transcripts, indicating breast cancer responsiveness and proliferation. Furthermore, DNA damage repair pathways were significantly upregulated in subtype 1. We performed in vitro and in vivo investigations, and found that cellular oxidative stress and further DNA damage existed in CTCs. The activated DNA damage repair pathway in CTCs favors resistance to cisplatin. A checkpoint kinase 1 inhibitor sensitized CTCs to cisplatin in mouse models of breast cancer metastasis. CONCLUSION The present study dissects the molecular characteristics of CTCs from early-stage breast cancer, providing novel insight into the understanding of CTC behavior in breast cancer metastasis.
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Affiliation(s)
- Shuyun Pang
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular MedicineMedical School of Nanjing UniversityNanjingChina
| | - Shu Xu
- School of Basic Medical Science and Clinical PharmacyChina Pharmaceutical UniversityNanjingChina
| | - Lulu Wang
- Department of General Surgery, Jinling HospitalMedical School of Nanjing UniversityNanjingChina
| | - Haiping Wu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular MedicineMedical School of Nanjing UniversityNanjingChina,School of Pharmaceutical ScienceSouthern Medical UniversityGuangzhouChina
| | - Yanan Chu
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular MedicineMedical School of Nanjing UniversityNanjingChina
| | - Xueping Ma
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular MedicineMedical School of Nanjing UniversityNanjingChina
| | - Yujiao Li
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular MedicineMedical School of Nanjing UniversityNanjingChina
| | - Bingjie Zou
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, School of PharmacyChina Pharmaceutical UniversityNanjingChina
| | - Shaohua Wang
- Department of General Surgery, Jinling HospitalMedical School of Nanjing UniversityNanjingChina
| | - Guohua Zhou
- Department of Clinical Pharmacy, Jinling Hospital, State Key Laboratory of Analytical Chemistry for Life Science & Jiangsu Key Laboratory of Molecular MedicineMedical School of Nanjing UniversityNanjingChina,School of Pharmaceutical ScienceSouthern Medical UniversityGuangzhouChina,School of PharmacyNanjing Medical UniversityNanjingChina
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McGinn O, Riley D, Finlay-Schultz J, Paul KV, Kabos P, Sartorius CA. Cytokeratins 5 and 17 Maintain an Aggressive Epithelial State in Basal-Like Breast Cancer. Mol Cancer Res 2022; 20:1443-1455. [PMID: 35639459 PMCID: PMC9444965 DOI: 10.1158/1541-7786.mcr-21-0866] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 04/18/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022]
Abstract
Basal-like breast cancers (BLBC) are the most common triple-negative subtype (hormone receptor and HER2 negative) with poor short-term disease outcome and are commonly identified by expression of basal cytokeratins (CK) 5 and 17. The goal of this study was to investigate whether CK5 and CK17 play a role in adverse behavior of BLBC cells. BLBC cell lines contain heterogeneous populations of cells expressing CK5, CK17, and the mesenchymal filament protein vimentin. Stable shRNA knockdown of either CK5 or CK17 compared with non-targeting control in BLBC cells was sufficient to promote an epithelial-mesenchymal transition (EMT) gene signature with loss of E-cadherin and an increase in vimentin expression. Relative to control cells, CK5 and CK17 knockdown cells acquired a more spindle-like morphology with increased cell scattering and were more invasive in vitro. However, CK5 or CK17 knockdown compared with control cells generated decreased lymph node and lung metastases in vivo. Loss of CK5 or CK17 moderately reduced the IC50 dose of doxorubicin in vitro and led to increased doxorubicin efficacy in vivo. Single-cell RNA-sequencing of BLBC patient-derived xenografts identified heterogeneous populations of CK5/CK17, vimentin, and dual basal CK/vimentin-positive cells that fell on an EMT spectrum of epithelial, mesenchymal, and intermediate, respectively, whereas knockdown of CK5 transitioned cells toward a more mesenchymal score. IMPLICATIONS This study supports that basal CKs 5 and 17 contribute to the adverse behavior of BLBC cells and could be an untapped source of therapeutic vulnerability for this aggressive disease.
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Affiliation(s)
- Olivia McGinn
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Duncan Riley
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Jessica Finlay-Schultz
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Kiran V. Paul
- Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Peter Kabos
- Department of Medicine, Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Carol A. Sartorius
- Department of Pathology, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
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Muraro E, Del Ben F, Turetta M, Cesselli D, Bulfoni M, Zamarchi R, Rossi E, Spazzapan S, Dolcetti R, Steffan A, Brisotto G. Clinical relevance of the combined analysis of circulating tumor cells and anti-tumor T-cell immunity in metastatic breast cancer patients. Front Oncol 2022; 12:983887. [PMID: 36081561 PMCID: PMC9446887 DOI: 10.3389/fonc.2022.983887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Background Metastatic breast cancer (mBC) is a heterogeneous disease with varying responses to treatments and clinical outcomes, still requiring the identification of reliable predictive biomarkers. In this context, liquid biopsy has emerged as a powerful tool to assess in real-time the evolving landscape of cancer, which is both orchestrated by the metastatic process and immune-surveillance mechanisms. Thus, we investigated circulating tumor cells (CTCs) coupled with peripheral T-cell immunity to uncover their potential clinical relevance in mBC. Methods A cohort of 20 mBC patients was evaluated, before and one month after starting therapy, through the following liquid biopsy approaches: CTCs enumerated by a metabolism-based assay, T-cell responses against tumor-associated antigens (TAA) characterized by interferon-γ enzyme-linked immunosorbent spot (ELISpot), and the T-cell receptor (TCR) repertoire investigated by a targeted next-generation sequencing technique. TCR repertoire features were characterized by the Morisita’s overlap and the Productive Simpson Clonality indexes, and the TCR richness. Differences between groups were calculated by Fisher’s, Mann-Whitney or Kruskal-Wallis test, as appropriate. Prognostic data analysis was estimated by Kaplan-Meier method. Results Stratifying patients for their prognostic level of 6 CTCs before therapy, TAA specific T-cell responses were detected only in patients with a low CTC level. By analyzing the TCR repertoire, the highest TCR clonality was observed in the case of CTCs under the cut-off and a positive ELISpot response (p=0.03). Whereas, at follow-up, patients showing a good clinical response coupled with a low number of CTCs were characterized by the most elevated TCR clonality (p<0.05). The detection of CTCs≥6 in at least one time-point was associated with a lower TCR clonality (p=0.02). Intriguingly, by combining overall survival analysis with TCR repertoire, we highlighted a potential prognostic role of the TCR clonality measured at follow-up (p=0.03). Conclusion These data, whether validated in a larger cohort of patients, suggest that the combined analysis of CTCs and circulating anti-tumor T-cell immunity could represent a valuable immune-oncological biomarker for the liquid biopsy field. The clinical application of this promising tool could improve the management of mBC patients, especially in the setting of immunotherapy, a rising approach for BC treatment requiring reliable predictive biomarkers.
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Affiliation(s)
- Elena Muraro
- Immunopathology and Cancer Biomarkers Units, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico, Aviano, Italy
- *Correspondence: Elena Muraro,
| | - Fabio Del Ben
- Department of Medicine, University of Udine, Udine, Italy
| | - Matteo Turetta
- Immunopathology and Cancer Biomarkers Units, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico, Aviano, Italy
| | - Daniela Cesselli
- Department of Medicine, University of Udine, Udine, Italy
- Institute of Pathology, University Hospital of Udine (Azienda sanitaria universitaria Friuli Centrale, ASUFC), Udine, Italy
| | - Michela Bulfoni
- Institute of Pathology, University Hospital of Udine (Azienda sanitaria universitaria Friuli Centrale, ASUFC), Udine, Italy
| | - Rita Zamarchi
- Department of Surgery, Oncology & Gastroenterology, University of Padova, Padua, Italy
| | - Elisabetta Rossi
- Department of Surgery, Oncology & Gastroenterology, University of Padova, Padua, Italy
- Veneto Institute of Oncology IOV - Istituto di Ricovero e Cura a Carattere Scientifico, Padua, Italy
| | - Simon Spazzapan
- Medical Oncology and Cancer Prevention Unit, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico, Aviano, Italy
| | - Riccardo Dolcetti
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC, Australia
- Department of Microbiology and Immunology, The University of Melbourne, Melbourne, VIC, Australia
- The University of Queensland Diamantina Institute, Brisbane, QLD, Australia
| | - Agostino Steffan
- Immunopathology and Cancer Biomarkers Units, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico, Aviano, Italy
| | - Giulia Brisotto
- Immunopathology and Cancer Biomarkers Units, Department of Translational Research, Centro di Riferimento Oncologico di Aviano (CRO), Istituto di Ricovero e Cura a Carattere Scientifico, Aviano, Italy
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10
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Ruan H, Wang Z, Sun Z, Wei J, Zhang L, Ju H, Wang T, Zhang C, Guan M, Pan S. Single-cell RNA sequencing reveals the characteristics of cerebrospinal fluid tumour environment in breast cancer and lung cancer leptomeningeal metastases. Clin Transl Med 2022; 12:e885. [PMID: 35678121 PMCID: PMC9178395 DOI: 10.1002/ctm2.885] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 04/28/2022] [Accepted: 05/04/2022] [Indexed: 11/23/2022] Open
Abstract
Leptomeningeal metastases (LM) occur in patients with breast cancer (BC) and lung cancer (LC) showing exceptionally poor prognosis. The cerebrospinal fluid (CSF) tumour microenvironment (TME) of LM patients is not well defined at a single‐cell level. Based on the 10× genomics single‐cell RNA sequencing (scRNA‐seq) data from GEO database including five patient‐derived CSF samples of BC‐LM and LC‐LM, and four patient‐derived CSF samples of idiopathic intracranial hypertension (IIH) as controls, we analysed single‐cell transcriptome characteristics of CSF TME in LM patients compared to controls simultaneously and comprehensively. In addition, we performed 10× genomics scRNA‐seq on CSF cells derived from a BC‐LM patient to help generate a solid conclusion. The CSF macrophages in LM patients showing M2‐subtype signature and the emergence of regulatory T cells in LM confirmed the direction of tumour immunity toward immunosuppression. Then, the characteristics of CSF circulating tumour cells (CTCs) of breast cancer LM (BC‐LM) patients were classified into five molecular subtypes by PAM50 model. The communication between macrophages and five subtype‐specific CSF‐CTCs showed largest number of ligand‐receptor interactions. The five subtypes‐specific CSF‐CTCs showed great heterogeneities which were manifested in cell proliferation and cancer‐testis antigens expression. Gene regulatory networks (GRNs) analysis revealed that transcription factor SREBF2 was universally activated in the five subtypes‐specific CSF‐CTCs. Our results will provide inspiration on new directions of the mechanism research, diagnosis and therapy of LM.
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Affiliation(s)
- Haoyu Ruan
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Zhe Wang
- Department of Physiology, Second Military Medical University, Shanghai, China
| | - Ziwei Sun
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jia Wei
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Lei Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Huanyu Ju
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Ting Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Chao Zhang
- Department of Plastic and Reconstructive Surgery, Shanghai Institute of Precision Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Fudan University, Shanghai, China
| | - Shiyang Pan
- Department of Laboratory Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, China.,Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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11
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Radfar P, Aboulkheyr Es H, Salomon R, Kulasinghe A, Ramalingam N, Sarafraz-Yazdi E, Thiery JP, Warkiani ME. Single-cell analysis of circulating tumour cells: enabling technologies and clinical applications. Trends Biotechnol 2022; 40:1041-1060. [DOI: 10.1016/j.tibtech.2022.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 02/15/2022] [Accepted: 02/16/2022] [Indexed: 11/26/2022]
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12
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Cucchiara F, Scarpitta R, Crucitta S, Scatena C, Arici R, Naccarato AG, Fogli S, Danesi R, Del Re M. Diagnosis and treatment monitoring in breast cancer: how liquid biopsy can support patient management. Pharmacogenomics 2022; 23:119-134. [PMID: 35006002 DOI: 10.2217/pgs-2021-0099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Imaging and tissue biopsies represent the current gold standard for breast cancer diagnosis and patient management. However, these practices are time-consuming, expensive and require invasive procedures. Moreover, tissue biopsies do not capture spatial and temporal tumor heterogeneity. Conversely, liquid biopsy, which includes circulating tumor cells, circulating free nucleic acids and extracellular vesicles, is minimally invasive, easy to perform and can be repeated during a patient's follow-up. Increasing evidence also suggests that liquid biopsy can be used to efficiently screen and diagnose tumors at an early stage, and to monitor changes in the tumor molecular profile. In the present review, clinical applications and prospects are discussed.
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Affiliation(s)
- Federico Cucchiara
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Rosa Scarpitta
- Division of Pathology, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa 56126, Italy
| | - Stefania Crucitta
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Cristian Scatena
- Division of Pathology, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa 56126, Italy
| | - Roberta Arici
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Antonio Giuseppe Naccarato
- Division of Pathology, Department of Translational Research & New Technologies in Medicine & Surgery, University of Pisa, Pisa 56126, Italy
| | - Stefano Fogli
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Romano Danesi
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
| | - Marzia Del Re
- Unit of Clinical Pharmacology & Pharmacogenetics, Department of Clinical & Experimental Medicine, University Hospital of Pisa, Pisa, Italy
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13
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Synergistic Analysis of Circulating Tumor Cells Reveals Prognostic Signatures in Pilot Study of Treatment-Naïve Metastatic Pancreatic Cancer Patients. Biomedicines 2022; 10:biomedicines10010146. [PMID: 35052825 PMCID: PMC8773204 DOI: 10.3390/biomedicines10010146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 01/02/2022] [Accepted: 01/04/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Pancreatic cancer is one of the most deadly cancer types because it usually is not diagnosed until the cancer has spread throughout the body. In this study, we isolate cancer cells found in the blood of pancreatic cancer patients called circulating tumor cells (CTCs) to study their mutation and gene expression profiles. Comparing patients with better and worse survival duration revealed signatures found in these cancer cells. Characterizing these signatures may help improve patient care by using alternative treatment options. Abstract Pancreatic ductal adenocarcinoma is typically diagnosed at late stages and has one of the lowest five-year survival rates of all malignancies. In this pilot study, we identify signatures related to survival and treatment response found in circulating tumor cells (CTCs). Patients with poor survival had increased mutant KRAS expression and deregulation of connected pathways such as PI3K-AKT and MAPK signaling. Further, in a subset of these patients, expression patterns of gemcitabine resistance mechanisms were observed, even prior to initiating treatment. This work highlights the need for identifying patients with these resistance profiles and designing treatment regimens to circumvent these mechanisms.
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14
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Lin D, Shen L, Luo M, Zhang K, Li J, Yang Q, Zhu F, Zhou D, Zheng S, Chen Y, Zhou J. Circulating tumor cells: biology and clinical significance. Signal Transduct Target Ther 2021; 6:404. [PMID: 34803167 PMCID: PMC8606574 DOI: 10.1038/s41392-021-00817-8] [Citation(s) in RCA: 347] [Impact Index Per Article: 115.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 10/06/2021] [Accepted: 10/27/2021] [Indexed: 02/07/2023] Open
Abstract
Circulating tumor cells (CTCs) are tumor cells that have sloughed off the primary tumor and extravasate into and circulate in the blood. Understanding of the metastatic cascade of CTCs has tremendous potential for the identification of targets against cancer metastasis. Detecting these very rare CTCs among the massive blood cells is challenging. However, emerging technologies for CTCs detection have profoundly contributed to deepening investigation into the biology of CTCs and have facilitated their clinical application. Current technologies for the detection of CTCs are summarized herein, together with their advantages and disadvantages. The detection of CTCs is usually dependent on molecular markers, with the epithelial cell adhesion molecule being the most widely used, although molecular markers vary between different types of cancer. Properties associated with epithelial-to-mesenchymal transition and stemness have been identified in CTCs, indicating their increased metastatic capacity. Only a small proportion of CTCs can survive and eventually initiate metastases, suggesting that an interaction and modulation between CTCs and the hostile blood microenvironment is essential for CTC metastasis. Single-cell sequencing of CTCs has been extensively investigated, and has enabled researchers to reveal the genome and transcriptome of CTCs. Herein, we also review the clinical applications of CTCs, especially for monitoring response to cancer treatment and in evaluating prognosis. Hence, CTCs have and will continue to contribute to providing significant insights into metastatic processes and will open new avenues for useful clinical applications.
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Affiliation(s)
- Danfeng Lin
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Breast Surgery, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Lesang Shen
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Meng Luo
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Kun Zhang
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jinfan Li
- Department of Pathology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Yang
- Department of Pathology, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Fangfang Zhu
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dan Zhou
- Department of Surgery, Traditional Chinese Medical Hospital of Zhuji, Shaoxing, China
| | - Shu Zheng
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yiding Chen
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Jiaojiao Zhou
- Department of Breast Surgery, the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
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15
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Liquid Biopsy Biomarkers for Immunotherapy in Non-Small Cell Lung Carcinoma: Lessons Learned and the Road Ahead. J Pers Med 2021; 11:jpm11100971. [PMID: 34683113 PMCID: PMC8540302 DOI: 10.3390/jpm11100971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/26/2022] Open
Abstract
Over the recent years, advances in the development of anti-cancer treatments, particularly the implementation of ICIs (immune checkpoint inhibitors), have resulted in increased survival rates in NSCLC (non-small cell lung cancer) patients. However, a significant proportion of patients does not seem respond to immunotherapy, and some individuals even develop secondary resistance to treatment. Therefore, it is imperative to correctly identify the patients that will benefit from ICI therapy in order to tailor therapeutic options in an individualised setting, ultimately benefitting both the patient and the health system. Many different biomarkers have been explored to correctly stratify patients and predict response to immunotherapy, but liquid biopsy approaches have recently arisen as an interesting opportunity to predict and monitor treatment response due to their logistic accessibility. This review summarises the current data and efforts in the field of ICI response biomarkers in NSCLC patients and highlights advantages and limitations as we discuss the road to clinical implementation.
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16
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Rossi T, Gallerani G, Martinelli G, Maltoni R, Fabbri F. Circulating Tumor Cells as a Tool to Untangle the Breast Cancer Heterogeneity Issue. Biomedicines 2021; 9:biomedicines9091242. [PMID: 34572427 PMCID: PMC8466266 DOI: 10.3390/biomedicines9091242] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 09/13/2021] [Accepted: 09/14/2021] [Indexed: 12/28/2022] Open
Abstract
Breast cancer (BC) is a disease characterized by high degrees of heterogeneity at morphologic, genomic, and genetic levels, even within the same tumor mass or among patients. As a consequence, different subpopulations coexist and less represented clones may have a selective advantage, significantly influencing the outcome of BC patients. Circulating tumor cells (CTCs) represent a rare population of cells with a crucial role in metastatic cascade, and in recent years have represented a fascinating alternative to overcome the heterogeneity issue as a “liquid biopsy”. However, besides the raw enumeration of these cells in advanced epithelial tumors, there are no CTC-based assays applied in the clinical practice to improve personalized medicine. In this review, we report the latest findings in the field of CTCs for intra-tumoral heterogeneity unmasking in BC, supporting the need to deepen their analysis to investigate their role in metastatic process and include the molecular characterization in the clinical practice. In the future, CTCs will be helpful in monitoring patients during treatment, as well as to better address therapeutic strategies.
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Affiliation(s)
- Tania Rossi
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (G.G.); (F.F.)
- Correspondence: ; Tel.: +39-0549-73-9982
| | - Giulia Gallerani
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (G.G.); (F.F.)
| | - Giovanni Martinelli
- Scientific Directorate, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy;
| | - Roberta Maltoni
- Healthcare Administration, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy;
| | - Francesco Fabbri
- Biosciences Laboratory, IRCCS Istituto Romagnolo per lo Studio dei Tumori (IRST) “Dino Amadori”, 47014 Meldola, Italy; (G.G.); (F.F.)
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17
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Menyailo ME, Bokova UA, Ivanyuk EE, Khozyainova AA, Denisov EV. Metastasis Prevention: Focus on Metastatic Circulating Tumor Cells. Mol Diagn Ther 2021; 25:549-562. [PMID: 34287797 DOI: 10.1007/s40291-021-00543-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2021] [Indexed: 12/13/2022]
Abstract
Metastasis is the main cause of cancer death. Metastatic foci are derived from tumor cells that detach from the primary tumor and then enter the circulation. Circulating tumor cells (CTCs) are generally associated with a high probability of distant metastasis and a negative prognosis. Most CTCs die in the bloodstream, and only a few cells form metastases. Such metastatic CTCs have a stem-like and hybrid epithelial-mesenchymal phenotype, can avoid immune surveillance, and show increased therapy resistance. Targeting metastatic CTCs and their progenitors in primary tumors and their descendants, particularly disseminated tumor cells, represents an attractive strategy for metastasis prevention. However, current therapeutic strategies mainly target the primary tumor and only indirectly affect metastasis-initiating cells. Here, we consider potential methods for preventing metastasis based on targeting molecular and cellular features of metastatic CTCs, including CTC clusters. Also, we emphasize current knowledge gaps in CTC biology that should be addressed to develop highly effective therapeutics and strategies for metastasis suppression.
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Affiliation(s)
- Maxim E Menyailo
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Kooperativny Str. 5, Tomsk, 634009, Russia
| | - Ustinia A Bokova
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Kooperativny Str. 5, Tomsk, 634009, Russia
| | - Elena E Ivanyuk
- Laboratory of Molecular Oncology and Immunology, Cancer Research Institute, Tomsk National Research Medical Center, Kooperativny Str. 5, Tomsk, 634009, Russia
| | - Anna A Khozyainova
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Kooperativny Str. 5, Tomsk, 634009, Russia
| | - Evgeny V Denisov
- Laboratory of Cancer Progression Biology, Cancer Research Institute, Tomsk National Research Medical Center, Kooperativny Str. 5, Tomsk, 634009, Russia.
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18
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Sun G, Li Z, Rong D, Zhang H, Shi X, Yang W, Zheng W, Sun G, Wu F, Cao H, Tang W, Sun Y. Single-cell RNA sequencing in cancer: Applications, advances, and emerging challenges. Mol Ther Oncolytics 2021; 21:183-206. [PMID: 34027052 PMCID: PMC8131398 DOI: 10.1016/j.omto.2021.04.001] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Cancer has become one of the greatest threats to human health, and new technologies are urgently needed to further clarify the mechanisms of cancer so that better detection and treatment strategies can be developed. At present, extensive genomic analysis and testing of clinical specimens shape the insights into carcinoma. Nevertheless, carcinoma of humans is a complex ecosystem of cells, including carcinoma cells and immunity-related and stroma-related subsets, with accurate characteristics obscured by extensive genome-related approaches. A growing body of research shows that sequencing of single-cell RNA (scRNA-seq) is emerging to be an effective way for dissecting human tumor tissue at single-cell resolution, presenting one prominent way for explaining carcinoma biology. This review summarizes the research progress of scRNA-seq in the field of tumors, focusing on the application of scRNA-seq in tumor circulating cells, tumor stem cells, tumor drug resistance, the tumor microenvironment, and so on, which provides a new perspective for tumor research.
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Affiliation(s)
- Guangshun Sun
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Zhouxiao Li
- Department of Hand Surgery, Plastic Surgery and Aesthetic Surgery, Ludwig Maximilians University, Munich, Germany
| | - Dawei Rong
- Hepatobiliary/Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Hao Zhang
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
- Department of Orthopedic Oncology, Shanghai Changzheng Hospital, Second Military Medical University, Shanghai, China
| | - Xuesong Shi
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weijun Yang
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wubin Zheng
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Guoqiang Sun
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Fan Wu
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Hongyong Cao
- Department of General Surgery, Nanjing First Hospital, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Weiwei Tang
- Hepatobiliary/Liver Transplantation Center, The First Affiliated Hospital of Nanjing Medical University, Key Laboratory of Living Donor Transplantation, Chinese Academy of Medical Sciences, Nanjing, Jiangsu, China
| | - Yangbai Sun
- Department of Musculoskeletal Surgery, Fudan University Shanghai Cancer Center, Shanghai Medical College, Fudan University, Shanghai, China
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19
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Lei Y, Tang R, Xu J, Wang W, Zhang B, Liu J, Yu X, Shi S. Applications of single-cell sequencing in cancer research: progress and perspectives. J Hematol Oncol 2021; 14:91. [PMID: 34108022 PMCID: PMC8190846 DOI: 10.1186/s13045-021-01105-2] [Citation(s) in RCA: 212] [Impact Index Per Article: 70.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Accepted: 06/03/2021] [Indexed: 02/06/2023] Open
Abstract
Single-cell sequencing, including genomics, transcriptomics, epigenomics, proteomics and metabolomics sequencing, is a powerful tool to decipher the cellular and molecular landscape at a single-cell resolution, unlike bulk sequencing, which provides averaged data. The use of single-cell sequencing in cancer research has revolutionized our understanding of the biological characteristics and dynamics within cancer lesions. In this review, we summarize emerging single-cell sequencing technologies and recent cancer research progress obtained by single-cell sequencing, including information related to the landscapes of malignant cells and immune cells, tumor heterogeneity, circulating tumor cells and the underlying mechanisms of tumor biological behaviors. Overall, the prospects of single-cell sequencing in facilitating diagnosis, targeted therapy and prognostic prediction among a spectrum of tumors are bright. In the near future, advances in single-cell sequencing will undoubtedly improve our understanding of the biological characteristics of tumors and highlight potential precise therapeutic targets for patients.
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Affiliation(s)
- Yalan Lei
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Rong Tang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jin Xu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Wei Wang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Bo Zhang
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Jiang Liu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China.,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China.,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China.,Pancreatic Cancer Institute, Fudan University, Shanghai, China
| | - Xianjun Yu
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China. .,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China. .,Pancreatic Cancer Institute, Fudan University, Shanghai, China.
| | - Si Shi
- Department of Pancreatic Surgery, Fudan University Shanghai Cancer Center, No. 270 Dong'An Road, Shanghai, 200032, China. .,Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China. .,Shanghai Pancreatic Cancer Institute, No. 270 Dong'An Road, Shanghai, 200032, China. .,Pancreatic Cancer Institute, Fudan University, Shanghai, China.
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20
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Bodlak A, Chang K, Channel J, Treece AL, Donaldson N, Cost CR, Garrington TP, Greffe B, Luna-Fineman S, Sopfe J, Loeb DM, Hayashi M. Circulating Plasma Tumor DNA Is Superior to Plasma Tumor RNA Detection in Ewing Sarcoma Patients: ptDNA and ptRNA in Ewing Sarcoma. J Mol Diagn 2021; 23:872-881. [PMID: 33887462 DOI: 10.1016/j.jmoldx.2021.04.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/11/2021] [Accepted: 04/08/2021] [Indexed: 11/25/2022] Open
Abstract
The detection of tumor-specific nucleic acids from blood increasingly is being used as a method of liquid biopsy and minimal residual disease detection. However, achieving high sensitivity and high specificity remains a challenge. Here, we perform a direct comparison of two droplet digital PCR (ddPCR)-based detection methods, circulating plasma tumor RNA and circulating plasma tumor DNA (ptDNA), in blood samples from newly diagnosed Ewing sarcoma patients. First, we developed three specific ddPCR-based assays to detect EWS-FLI1 or EWS-ERG fusion transcripts, which naturally showed superior sensitivity to DNA detection on in vitro control samples. Next, we identified the patient-specific EWS-FLI1 or EWS-ERG breakpoint from five patient tumor samples and designed ddPCR-based, patient-specific ptDNA assays for each patient. These patient-specific assays show that although plasma tumor RNA can be detected in select newly diagnosed patients, positive results are low and statistically unreliable compared with ptDNA assays, which reproducibly detect robust positive results across most patients. Furthermore, the unique disease biology of Ewing sarcoma enabled us to show that most cell-free RNA is not tumor-derived, although cell-free-DNA burden is affected strongly by tumor-derived DNA burden. Here, we conclude that, even with optimized highly sensitive and specific assays, tumor DNA detection is superior to RNA detection in Ewing sarcoma patients.
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Affiliation(s)
- Avery Bodlak
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado
| | - Kyle Chang
- Department of Biology and Biochemistry, University of Houston, Houston, Texas
| | - Jessica Channel
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado
| | - Amy L Treece
- Department of Pathology, University of Colorado Denver, Aurora, Colorado
| | - Nathan Donaldson
- Department of Orthopedics, University of Colorado Denver, Aurora, Colorado
| | - Carrye R Cost
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado
| | | | - Brian Greffe
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado
| | | | - Jenna Sopfe
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado
| | - David M Loeb
- Department of Pediatrics, Albert Einstein College of Medicine, New York, New York
| | - Masanori Hayashi
- Department of Pediatrics, University of Colorado Denver, Aurora, Colorado.
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21
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Liu J, Xu T, Jin Y, Huang B, Zhang Y. Progress and Clinical Application of Single-Cell Transcriptional Sequencing Technology in Cancer Research. Front Oncol 2021; 10:593085. [PMID: 33614479 PMCID: PMC7886993 DOI: 10.3389/fonc.2020.593085] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2020] [Accepted: 12/21/2020] [Indexed: 12/15/2022] Open
Abstract
Cancer has been a daunting challenge for human beings because of its clonal heterogeneity and compositional complexity. Tumors are composed of cancer cells and a variety of non-cancer cells, which together with the extracellular matrix form the tumor microenvironment. These cancer-related cells and components and immune mechanisms can affect the development and progression of cancer and are associated with patient diagnosis, treatment and prognosis. As the first choice for the study of complex biological systems, single-cell transcriptional sequencing (scRNA-seq) has been widely used in cancer research. ScRNA-seq has made breakthrough discoveries in tumor heterogeneity, tumor evolution, metastasis and spread, development of chemoresistance, and the relationship between the tumor microenvironment and the immune system. These results will guide clinical cancer treatment and promote personalized and highly accurate cancer treatment. In this paper, we summarize the latest research progress of scRNA-seq and its guiding significance for clinical treatment.
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Affiliation(s)
- Jian Liu
- Department of Gynaecology and Obstetrics, Jilin University Second Hospital, ChangChun, China
| | - Tianmin Xu
- Department of Gynaecology and Obstetrics, Jilin University Second Hospital, ChangChun, China
| | - Yuemei Jin
- Department of Gynaecology and Obstetrics, Jilin University Second Hospital, ChangChun, China
| | - Bingyu Huang
- Department of Gynaecology and Obstetrics, Jilin University Second Hospital, ChangChun, China
| | - Yan Zhang
- Department of Breast Surgery, Jilin University Second Hospital, ChangChun, China
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22
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Badia-Ramentol J, Linares J, Gómez-Llonin A, Calon A. Minimal Residual Disease, Metastasis and Immunity. Biomolecules 2021; 11:130. [PMID: 33498251 PMCID: PMC7909268 DOI: 10.3390/biom11020130] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/11/2022] Open
Abstract
Progression from localized to metastatic disease requires cancer cells spreading to distant organs through the bloodstream. Only a small proportion of these circulating tumor cells (CTCs) survives dissemination due to anoikis, shear forces and elimination by the immune system. However, all metastases originate from CTCs capable of surviving and extravasating into distant tissue to re-initiate a tumor. Metastasis initiation is not always immediate as disseminated tumor cells (DTCs) may enter a non-dividing state of cell dormancy. Cancer dormancy is a reversible condition that can be maintained for many years without being clinically detectable. Subsequently, late disease relapses are thought to be due to cancer cells ultimately escaping from dormant state. Cancer dormancy is usually associated with minimal residual disease (MRD), where DTCs persist after intended curative therapy. Thus, MRD is commonly regarded as an indicator of poor prognosis in all cancers. In this review, we examine the current understanding of MRD and immunity during cancer progression to metastasis and discuss clinical perspectives for oncology.
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Affiliation(s)
| | | | | | - Alexandre Calon
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), 08003 Barcelona, Spain; (J.B.-R.); (J.L.); (A.G.-L.)
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23
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Dai Z, Gu XY, Xiang SY, Gong DD, Man CF, Fan Y. Research and application of single-cell sequencing in tumor heterogeneity and drug resistance of circulating tumor cells. Biomark Res 2020; 8:60. [PMID: 33292625 PMCID: PMC7653877 DOI: 10.1186/s40364-020-00240-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 10/29/2020] [Indexed: 02/06/2023] Open
Abstract
Malignant tumor is a largely harmful disease worldwide. The cure rate of malignant tumors increases with the continuous discovery of anti-tumor drugs and the optimisation of chemotherapy options. However, drug resistance of tumor cells remains a massive obstacle in the treatment of anti-tumor drugs. The heterogeneity of malignant tumors makes studying it further difficult for us. In recent years, using single-cell sequencing technology to study and analyse circulating tumor cells can avoid the interference of tumor heterogeneity and provide a new perspective for us to understand tumor drug resistance.
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Affiliation(s)
- Zhe Dai
- Cancer Institution, Affiliated People’s Hospital of Jiangsu University, No.8 Dianli Road, Zhenjiang, Jiangsu Province 212002 People’s Republic of China
| | - Xu-yu Gu
- Cancer Institution, Affiliated People’s Hospital of Jiangsu University, No.8 Dianli Road, Zhenjiang, Jiangsu Province 212002 People’s Republic of China
| | - Shou-yan Xiang
- Cancer Institution, Affiliated People’s Hospital of Jiangsu University, No.8 Dianli Road, Zhenjiang, Jiangsu Province 212002 People’s Republic of China
| | - Dan-dan Gong
- Cancer Institution, Affiliated People’s Hospital of Jiangsu University, No.8 Dianli Road, Zhenjiang, Jiangsu Province 212002 People’s Republic of China
| | - Chang-feng Man
- Cancer Institution, Affiliated People’s Hospital of Jiangsu University, No.8 Dianli Road, Zhenjiang, Jiangsu Province 212002 People’s Republic of China
| | - Yu Fan
- Cancer Institution, Affiliated People’s Hospital of Jiangsu University, No.8 Dianli Road, Zhenjiang, Jiangsu Province 212002 People’s Republic of China
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24
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Tabor S, Szostakowska-Rodzos M, Fabisiewicz A, Grzybowska EA. How to Predict Metastasis in Luminal Breast Cancer? Current Solutions and Future Prospects. Int J Mol Sci 2020; 21:ijms21218415. [PMID: 33182512 PMCID: PMC7665153 DOI: 10.3390/ijms21218415] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 10/28/2020] [Accepted: 11/07/2020] [Indexed: 12/12/2022] Open
Abstract
Breast cancer metastasis is the main cause of breast cancer mortality. Luminal breast cancer represents the majority of breast cancer cases and, despite relatively good prognosis, its heterogeneity creates problems with a proper stratification of patients and correct identification of the group with a high risk of metastatic relapse. Current prognostic tools are based on the analysis of the primary tumor and, despite their undisputed power of prediction, they might be insufficient to foresee the relapse in an accurate and precise manner, especially if the relapse occurs after a long period of dormancy, which is very common in luminal breast cancer. New approaches tend to rely on body fluid analyses, which have the advantage of being non-invasive and versatile and may be repeated and used for monitoring the disease in the long run. In this review we describe the current, newly-developed, and only-just-discovered methods which are or may become useful in the assessment of the probability of the relapse.
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