1
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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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2
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Lim J, Chin V, Fairfax K, Moutinho C, Suan D, Ji H, Powell JE. Transitioning single-cell genomics into the clinic. Nat Rev Genet 2023:10.1038/s41576-023-00613-w. [PMID: 37258725 DOI: 10.1038/s41576-023-00613-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/02/2023] [Indexed: 06/02/2023]
Abstract
The use of genomics is firmly established in clinical practice, resulting in innovations across a wide range of disciplines such as genetic screening, rare disease diagnosis and molecularly guided therapy choice. This new field of genomic medicine has led to improvements in patient outcomes. However, most clinical applications of genomics rely on information generated from bulk approaches, which do not directly capture the genomic variation that underlies cellular heterogeneity. With the advent of single-cell technologies, research is rapidly uncovering how genomic data at cellular resolution can be used to understand disease pathology and mechanisms. Both DNA-based and RNA-based single-cell technologies have the potential to improve existing clinical applications and open new application spaces for genomics in clinical practice, with oncology, immunology and haematology poised for initial adoption. However, challenges in translating cellular genomics from research to a clinical setting must first be overcome.
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Affiliation(s)
- Jennifer Lim
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Department of Oncology, St George Hospital, Sydney, NSW, Australia
- The Kinghorn Cancer Centre, St Vincent's Hospital, Sydney, NSW, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Venessa Chin
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
- The Kinghorn Cancer Centre, St Vincent's Hospital, Sydney, NSW, Australia
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Kirsten Fairfax
- School of Medicine, University of Tasmania, Hobart, Australia
| | - Catia Moutinho
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
| | - Dan Suan
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia
- Westmead Clinical School, University of Sydney, Sydney, NSW, Australia
| | - Hanlee Ji
- School of Medicine, Stanford University, Palo Alto, CA, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
| | - Joseph E Powell
- Cellular Science, Garvan Institute of Medical Research, Sydney, NSW, Australia.
- Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia.
- UNSW Cellular Genomics Futures Institute, University of New South Wales, Sydney, NSW, Australia.
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3
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Hayat A, Carter EP, King HW, Ors A, Doe A, Teijeiro SA, Charrot S, Godinho S, Cutillas P, Mohammed H, Grose RP, Ficz G. Low HER2 expression in normal breast epithelium enables dedifferentiation and malignant transformation via chromatin opening. Dis Model Mech 2023; 16:dmm049894. [PMID: 36661191 PMCID: PMC9922733 DOI: 10.1242/dmm.049894] [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: 09/20/2022] [Accepted: 01/06/2023] [Indexed: 01/21/2023] Open
Abstract
Overexpression of the HER2 protein in breast cancer patients is a predictor of poor prognosis and resistance to therapies. We used an inducible breast cancer transformation system that allows investigation of early molecular changes. HER2 overexpression to similar levels as those observed in a subtype of HER2-positive breast cancer patients induced transformation of MCF10A cells and resulted in gross morphological changes, increased anchorage-independent growth of cells, and altered the transcriptional programme of genes associated with oncogenic transformation. Global phosphoproteomic analysis during HER2 induction predominantly detected an increase in protein phosphorylation. Intriguingly, this correlated with chromatin opening, as measured by ATAC-seq on acini isolated from 3D cell culture. HER2 overexpression resulted in opening of many distal regulatory regions and promoted reprogramming-associated heterogeneity. We found that a subset of cells acquired a dedifferentiated breast stem-like phenotype, making them likely candidates for malignant transformation. Our data show that this population of cells, which counterintuitively enriches for relatively low HER2 protein abundance and increased chromatin accessibility, possesses transformational drive, resulting in increased anchorage-independent growth in vitro compared to cells not displaying a stem-like phenotype.
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Affiliation(s)
- Ateequllah Hayat
- Institute of Medical and Biomedical Education, St George’s, University of London, Cranmer Terrace, Tooting, London SW17 0RE, UK
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Edward P. Carter
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Hamish W. King
- Epigenetics and Development Division, Walter and Eliza Hall Institute of Medical Research, Royal Parade, Parkville, VIC 3052, Australia
| | - Aysegul Ors
- Knight Cancer Institute, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239-3098, USA
| | - Aaron Doe
- Knight Cancer Institute, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239-3098, USA
| | - Saul A. Teijeiro
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Sarah Charrot
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Susana Godinho
- Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Pedro Cutillas
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Hisham Mohammed
- Knight Cancer Institute, Oregon Health and Science University, 3181 S.W. Sam Jackson Park Road, Portland, OR 97239-3098, USA
| | - Richard P. Grose
- Centre for Tumour Biology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
| | - Gabriella Ficz
- Centre for Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK
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4
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Lunardi M, Al-Habbaa A, Abdelshafy M, Davey MG, Elkoumy A, Ganly S, Elzomor H, Cawley C, Sharif F, Crowley J, Kerin M, Wijns W, Lowery A, Soliman O. Genetic and RNA-related molecular markers of trastuzumab-chemotherapy-associated cardiotoxicity in HER2 positive breast cancer: a systematic review. BMC Cancer 2022; 22:396. [PMID: 35413811 PMCID: PMC9004047 DOI: 10.1186/s12885-022-09437-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 03/16/2022] [Indexed: 11/19/2022] Open
Abstract
Cancer-therapy related cardiotoxicity (CTRCT) is a significant and frequent complication of monoclonal antibody directed therapy, especially Trastuzumab, for human epidermal growth factor receptor 2 (HER2) overexpressing breast cancers. Reliable, clinically available molecular predictive markers of CTRCT have not yet been developed. Identifying specific genetic variants and their molecular markers, which make the host susceptible to this complication is key to personalised risk stratification. A systematic review was conducted until April 2021, using the Medline, Embase databases and Google Scholar, to identify studies genetic and RNA-related markers associated with CTRCT in HER2 positive breast cancer patients. So far, researchers have mainly focused on HER2 related polymorphisms, revealing codons 655 and 1170 variants as the most likely SNPs associated with cardiotoxicity, despite some contradictory results. More recently, new potential genetic markers unrelated to the HER2 gene, and linked to known cardiomyopathy genes or to genes regulating cardiomyocytes apoptosis and metabolism, have been detected. Moreover, microRNAs are gaining increasing recognition as additional potential molecular markers in the cardio-oncology field, supported by encouraging preliminary data about their relationship with cardiotoxicity in breast cancers. In this review, we sought to synthesize evidence for genetic variants and RNA-related molecular markers associated with cardiotoxicity in HER2-positive breast cancer.
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Affiliation(s)
- Mattia Lunardi
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland.,Division of Cardiology, Department of Medicine, University of Verona, Verona, Italy.,The Lambe Institute for Translational Medicine and CURAM, National University of Ireland Galway (NUIG), Galway, Ireland
| | - Ahmed Al-Habbaa
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland.,Department of Cardiology, Faculty of Medicine, Al-Azhar University, Cairo, Egypt
| | - Mahmoud Abdelshafy
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland
| | - Matthew G Davey
- Discipline of Surgery, School of Medicine, Lambe Institute for Translational Research, National University of Ireland Galway, Galway, Ireland
| | - Ahmed Elkoumy
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland
| | - Sandra Ganly
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland.,The Lambe Institute for Translational Medicine and CURAM, National University of Ireland Galway (NUIG), Galway, Ireland.,Precision Cardio-Oncology Research Enterprise (P-CORE), National University of Ireland, Galway, Ireland
| | - Hesham Elzomor
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland
| | - Christian Cawley
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland
| | - Faisal Sharif
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland
| | - James Crowley
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland
| | - Michael Kerin
- Discipline of Surgery, School of Medicine, Lambe Institute for Translational Research, National University of Ireland Galway, Galway, Ireland.,Precision Cardio-Oncology Research Enterprise (P-CORE), National University of Ireland, Galway, Ireland
| | - William Wijns
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland.,The Lambe Institute for Translational Medicine and CURAM, National University of Ireland Galway (NUIG), Galway, Ireland.,Precision Cardio-Oncology Research Enterprise (P-CORE), National University of Ireland, Galway, Ireland
| | - Aoife Lowery
- Discipline of Surgery, School of Medicine, Lambe Institute for Translational Research, National University of Ireland Galway, Galway, Ireland.,Precision Cardio-Oncology Research Enterprise (P-CORE), National University of Ireland, Galway, Ireland
| | - Osama Soliman
- Discipline of Cardiology, Saolta Group, Galway University Hospital, Health Service Executive and CORRIB Core Lab, National University of Ireland Galway (NUIG), Galway, H91 TK33, Ireland. .,Precision Cardio-Oncology Research Enterprise (P-CORE), National University of Ireland, Galway, Ireland.
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5
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Lovero D, D’Oronzo S, Palmirotta R, Cafforio P, Brown J, Wood S, Porta C, Lauricella E, Coleman R, Silvestris F. Correlation between targeted RNAseq signature of breast cancer CTCs and onset of bone-only metastases. Br J Cancer 2022; 126:419-429. [PMID: 34272498 PMCID: PMC8810805 DOI: 10.1038/s41416-021-01481-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/04/2021] [Accepted: 06/30/2021] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Bone is the most frequent site of metastases from breast cancer (BC), but no biomarkers are yet available to predict skeletal dissemination. METHODS We attempted to identify a gene signature correlated with bone metastasis (BM) onset in circulating tumour cells (CTCs), isolated by a DEPArray-based protocol from 40 metastatic BC patients and grouped according to metastasis sites, namely "BM" (bone-only), "ES" (extra-skeletal) or BM + ES (bone + extra-skeletal). RESULTS A 134-gene panel was first validated through targeted RNA sequencing (RNAseq) on sub-clones of the MDA-MB-231 BC cell line with variable organotropism, which successfully shaped their clustering. The panel was then applied to CTC groups and, in particular, the "BM" vs "ES" CTC comparison revealed 31 differentially expressed genes, including MAF, CAPG, GIPC1 and IL1B, playing key prognostic roles in BC. CONCLUSION Such evidence confirms that CTCs are suitable biological sources for organotropism investigation through targeted RNAseq and might deserve future applications in wide-scale prospective studies.
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Affiliation(s)
- Domenica Lovero
- grid.7644.10000 0001 0120 3326Department of Biomedical Sciences and Human Oncology—Section of Internal Medicine and Clinical Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Stella D’Oronzo
- grid.7644.10000 0001 0120 3326Department of Biomedical Sciences and Human Oncology—Section of Internal Medicine and Clinical Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Raffaele Palmirotta
- grid.7644.10000 0001 0120 3326Department of Biomedical Sciences and Human Oncology—Section of Internal Medicine and Clinical Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Paola Cafforio
- grid.7644.10000 0001 0120 3326Department of Biomedical Sciences and Human Oncology—Section of Internal Medicine and Clinical Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Janet Brown
- grid.417079.c0000 0004 0391 9207Department of Oncology and Metabolism, University of Sheffield, Weston Park Hospital, Sheffield, UK
| | - Steven Wood
- grid.417079.c0000 0004 0391 9207Department of Oncology and Metabolism, University of Sheffield, Weston Park Hospital, Sheffield, UK
| | - Camillo Porta
- grid.7644.10000 0001 0120 3326Department of Biomedical Sciences and Human Oncology—Section of Internal Medicine and Clinical Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Eleonora Lauricella
- grid.7644.10000 0001 0120 3326Department of Biomedical Sciences and Human Oncology—Section of Internal Medicine and Clinical Oncology, University of Bari Aldo Moro, Bari, Italy
| | - Robert Coleman
- grid.417079.c0000 0004 0391 9207Department of Oncology and Metabolism, University of Sheffield, Weston Park Hospital, Sheffield, UK
| | - Franco Silvestris
- grid.7644.10000 0001 0120 3326Department of Biomedical Sciences and Human Oncology—Section of Internal Medicine and Clinical Oncology, University of Bari Aldo Moro, Bari, Italy
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6
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Kaboli PJ, Imani S, Jomhori M, Ling KH. Chemoresistance in breast cancer: PI3K/Akt pathway inhibitors vs the current chemotherapy. Am J Cancer Res 2021; 11:5155-5183. [PMID: 34765318 PMCID: PMC8569340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/12/2021] [Indexed: 06/13/2023] Open
Abstract
Breast cancer is the most prevalent type of cancer among women. Several types of drugs, targeting the specific proteins expressed on the breast cancer cell surface (such as receptor tyrosine kinases and immune checkpoint regulators) and proteins involved in cell cycle and motility (including cyclin-dependent kinases, DNA stabilisers, and cytoskeleton modulators) are approved for different subtypes of breast cancer. However, breast cancer also has a poor response to conventional chemotherapy due to intrinsic and acquired resistance, and an Akt fingerprint is detectable in most drug-resistant cases. Overactivation of Akt and its upstream and downstream regulators in resistant breast cancer cells is considered a major potential target for novel anti-cancer therapies, suggesting that Akt signalling acts as a cellular mechanism against chemotherapy. The present review has shown that sustained activation of Akt results in resistance to different types of chemotherapy. Akt signalling plays a cellular defence role against chemotherapy and (1) enhances multi-drug resistance, (2) increases reactive oxygen species at breast tumor microenvironment, (3) enhances anaerobic metabolism, (4) inhibits the tricarboxylic cycle, (5) promotes PD-L1 upregulation, (6) inhibits apoptosis, (7) increases glucose uptake, and more importantly (8) recruits and interconnects the plasma membrane, nucleus, endoplasmic reticulum, and mitochondria to hijack breast cancer cells and rescue these cells from chemotherapy. Therefore, Akt signalling is considered a cellular defence mechanism employed against chemotherapeutic effects. In addition, interfering roles of PI3K/Akt signalling on the current cytotoxic and molecularly targeted therapy as well as immunotherapy of breast cancer are discussed with a clinical approach. Although, alpelisib, a PIK3CA inhibitor, is the only PI3K/Akt pathway inhibitor approved for breast cancer, we also highlight well-evaluated inhibitors of PI3K/Akt signalling based on different subtypes of breast cancer, which are under clinical trials whether as monotherapy or in combination with other types of chemotherapy.
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Affiliation(s)
- Parham Jabbarzadeh Kaboli
- Graduate Institute of Biomedical Sciences, Research Center for Cancer Biology, and Center for Molecular Medicine, China Medical UniversityTaichung 404, Taiwan
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra MalaysiaSerdang, Selangor 43400, Malaysia
| | - Saber Imani
- Department of Oncology, The Affiliated Hospital of Southwest Medical UniversityLuzhou, Sichuan 646000, P. R. China
| | - Masume Jomhori
- Department of Biotechnology Research, Razi Vaccine and Serum Research InstituteMashhad, Iran
| | - King-Hwa Ling
- Department of Biomedical Science, Faculty of Medicine and Health Sciences, Universiti Putra MalaysiaSerdang, Selangor 43400, Malaysia
- Department of Genetics, Harvard Medical SchoolBoston, MA 02115, USA
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7
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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: 185] [Impact Index Per Article: 61.7] [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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8
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Thomas D, Shenoy S, Sayed N. Building Multi-Dimensional Induced Pluripotent Stem Cells-Based Model Platforms to Assess Cardiotoxicity in Cancer Therapies. Front Pharmacol 2021; 12:607364. [PMID: 33679396 PMCID: PMC7930625 DOI: 10.3389/fphar.2021.607364] [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: 09/17/2020] [Accepted: 01/06/2021] [Indexed: 02/06/2023] Open
Abstract
Cardiovascular disease (CVD) complications have contributed significantly toward poor survival of cancer patients worldwide. These complications that result in myocardial and vascular damage lead to long-term multisystemic disorders. In some patient cohorts, the progression from acute to symptomatic CVD state may be accelerated due to exacerbation of underlying comorbidities such as obesity, diabetes and hypertension. In such situations, cardio-oncologists are often left with a clinical predicament in finding the optimal therapeutic balance to minimize cardiovascular risks and maximize the benefits in treating cancer. Hence, prognostically there is an urgent need for cost-effective, rapid, sensitive and patient-specific screening platform to allow risk-adapted decision making to prevent cancer therapy related cardiotoxicity. In recent years, momentous progress has been made toward the successful derivation of human cardiovascular cells from induced pluripotent stem cells (iPSCs). This technology has not only provided deeper mechanistic insights into basic cardiovascular biology but has also seamlessly integrated within the drug screening and discovery programs for early efficacy and safety evaluation. In this review, we discuss how iPSC-derived cardiovascular cells have been utilized for testing oncotherapeutics to pre-determine patient predisposition to cardiovascular toxicity. Lastly, we highlight the convergence of tissue engineering technologies and precision medicine that can enable patient-specific cardiotoxicity prognosis and treatment on a multi-organ level.
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Affiliation(s)
- Dilip Thomas
- Stanford Cardiovascular Institute, Stanford, CA, United States.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, United States
| | - Sushma Shenoy
- Stanford Cardiovascular Institute, Stanford, CA, United States
| | - Nazish Sayed
- Stanford Cardiovascular Institute, Stanford, CA, United States.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford, CA, United States.,Division of Vascular Surgery, Department of Surgery, Stanford University School of Medicine, Stanford, CA, United States
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9
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Therapy-Induced Evolution of Human Lung Cancer Revealed by Single-Cell RNA Sequencing. Cell 2020; 182:1232-1251.e22. [PMID: 32822576 PMCID: PMC7484178 DOI: 10.1016/j.cell.2020.07.017] [Citation(s) in RCA: 323] [Impact Index Per Article: 80.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 05/04/2020] [Accepted: 07/13/2020] [Indexed: 02/06/2023]
Abstract
Lung cancer, the leading cause of cancer mortality, exhibits heterogeneity that enables adaptability, limits therapeutic success, and remains incompletely understood. Single-cell RNA sequencing (scRNA-seq) of metastatic lung cancer was performed using 49 clinical biopsies obtained from 30 patients before and during targeted therapy. Over 20,000 cancer and tumor microenvironment (TME) single-cell profiles exposed a rich and dynamic tumor ecosystem. scRNA-seq of cancer cells illuminated targetable oncogenes beyond those detected clinically. Cancer cells surviving therapy as residual disease (RD) expressed an alveolar-regenerative cell signature suggesting a therapy-induced primitive cell-state transition, whereas those present at on-therapy progressive disease (PD) upregulated kynurenine, plasminogen, and gap-junction pathways. Active T-lymphocytes and decreased macrophages were present at RD and immunosuppressive cell states characterized PD. Biological features revealed by scRNA-seq were biomarkers of clinical outcomes in independent cohorts. This study highlights how therapy-induced adaptation of the multi-cellular ecosystem of metastatic cancer shapes clinical outcomes. scRNA-seq is feasible in metastatic human NSCLCs and reveals a rich tumor ecosystem Individual tumors and cancer cells exhibit substantial molecular diversity Cancer and tumor microenvironment cells exhibit marked therapy-induced plasticity scRNA-seq of metastatic NSCLCs unveils new opportunities to improve clinical outcomes
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Ding S, Chen X, Shen K. Single-cell RNA sequencing in breast cancer: Understanding tumor heterogeneity and paving roads to individualized therapy. Cancer Commun (Lond) 2020; 40:329-344. [PMID: 32654419 PMCID: PMC7427308 DOI: 10.1002/cac2.12078] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2020] [Revised: 06/27/2020] [Accepted: 06/29/2020] [Indexed: 12/18/2022] Open
Abstract
Single‐cell RNA sequencing (scRNA‐seq) is a novel technology that allows transcriptomic analyses of individual cells. During the past decade, scRNA‐seq sensitivity, accuracy, and efficiency have improved due to innovations including more sensitive, automated, and cost‐effective single‐cell isolation methods with higher throughput as well as ongoing technological development of scRNA‐seq protocols. Among the variety of current approaches with distinct features, researchers can choose the most suitable method to carry out their research. By profiling single cells in a complex population mix, scRNA‐seq presents great advantages over traditional sequencing methods in dissecting heterogeneity in cell populations hidden in bulk analysis and exploring rare cell types associated with tumorigenesis and metastasis. scRNA‐seq studies in recent years in the field of breast cancer research have clustered breast cancer cell populations with different molecular subtypes to identify distinct populations that may correlate with poor prognosis and drug resistance. The technology has also been used to explain tumor microenvironment heterogeneity by identifying distinct immune cell subsets that may be associated with immunosurveillance and are potential immunotherapy targets. Moreover, scRNA‐seq has diverse applications in breast cancer research besides exploring heterogeneity, including the analysis of cell‐cell communications, regulatory single‐cell states, immune cell distributions, and more. scRNA‐seq is also a promising tool that can facilitate individualized therapy due to its ability to define cell subsets with potential treatment targets. Although scRNA‐seq studies of therapeutic selection in breast cancer are currently limited, the application of this technology in this field is prospective. Joint efforts and original ideas are needed to better implement scRNA‐seq technologies in breast cancer research to pave the way for individualized treatment management. This review provides a brief introduction on the currently available scRNA‐seq approaches along with their corresponding strengths and weaknesses and may act as a reference for the selection of suitable methods for research. We also discuss the current applications of scRNA‐seq in breast cancer research for tumor heterogeneity analysis, individualized therapy, and the other research directions mentioned above by reviewing corresponding published studies. Finally, we discuss the limitations of current scRNA‐seq technologies and technical problems that remain to be overcome.
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Affiliation(s)
- Shuning Ding
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Xiaosong Chen
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
| | - Kunwei Shen
- Department of General Surgery, Comprehensive Breast Health Center, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, P. R. China
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Kamies R, Martinez-Jimenez CP. Advances of single-cell genomics and epigenomics in human disease: where are we now? Mamm Genome 2020; 31:170-180. [PMID: 32270277 PMCID: PMC7368869 DOI: 10.1007/s00335-020-09834-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/28/2020] [Indexed: 02/07/2023]
Abstract
Cellular heterogeneity is revolutionizing the way to study, monitor and dissect complex diseases. This has been possible with the technological and computational advances associated to single-cell genomics and epigenomics. Deeper understanding of cell-to-cell variation and its impact on tissue function will open new avenues for early disease detection, accurate diagnosis and personalized treatments, all together leading to the next generation of health care. This review focuses on the recent discoveries that single-cell genomics and epigenomics have facilitated in the context of human health. It highlights the potential of single-cell omics to further advance the development of personalized treatments and precision medicine in cancer, diabetes and chronic age-related diseases. The promise of single-cell technologies to generate new insights about the differences in function between individual cells is just emerging, and it is paving the way for identifying biomarkers and novel therapeutic targets to tackle age, complex diseases and understand the effect of life style interventions and environmental factors.
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Affiliation(s)
- Rizqah Kamies
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany
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12
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Conforte AJ, Alves L, Coelho FC, Carels N, da Silva FAB. Modeling Basins of Attraction for Breast Cancer Using Hopfield Networks. Front Genet 2020; 11:314. [PMID: 32318098 PMCID: PMC7154169 DOI: 10.3389/fgene.2020.00314] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/16/2020] [Indexed: 12/26/2022] Open
Abstract
Cancer is a genetic disease for which traditional treatments cause harmful side effects. After two decades of genomics technological breakthroughs, personalized medicine is being used to improve treatment outcomes and mitigate side effects. In mathematical modeling, it has been proposed that cancer matches an attractor in Waddington's epigenetic landscape. The use of Hopfield networks is an attractive modeling approach because it requires neither previous biological knowledge about protein-protein interactions nor kinetic parameters. In this report, Hopfield network modeling was used to analyze bulk RNA-Seq data of paired breast tumor and control samples from 70 patients. We characterized the control and tumor attractors with respect to their size and potential energy and correlated the Euclidean distances between the tumor samples and the control attractor with their corresponding clinical data. In addition, we developed a protocol that outlines the key genes involved in tumor state stability. We found that the tumor basin of attraction is larger than that of the control and that tumor samples are associated with a more substantial negative energy than control samples, which is in agreement with previous reports. Moreover, we found a negative correlation between the Euclidean distances from tumor samples to the control attractor and patient overall survival. The ascending order of each node's density in the weight matrix and the descending order of the number of patients that have the target active only in the tumor sample were the parameters that withdrew more tumor samples from the tumor basin of attraction with fewer gene inhibitions. The combinations of therapeutic targets were specific to each patient. We performed an initial validation through simulation of trastuzumab treatment effects in HER2+ breast cancer samples. For that, we built an energy landscape composed of single-cell and bulk RNA-Seq data from trastuzumab-treated and non-treated HER2+ samples. The trajectory from the non-treated bulk sample toward the treated bulk sample was inferred through the perturbation of differentially expressed genes between these samples. Among them, we characterized key genes involved in the trastuzumab response according to the literature.
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Affiliation(s)
- Alessandra Jordano Conforte
- Laboratory of Biological Systems Modeling, Center for Technological Development in Health, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil.,Laboratory of Computational Modeling of Biological Systems, Scientific Computing Program, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Leon Alves
- Applied Math School, Getúlio Vargas Foundation, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | | | - Nicolas Carels
- Laboratory of Biological Systems Modeling, Center for Technological Development in Health, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
| | - Fabrício Alves Barbosa da Silva
- Laboratory of Computational Modeling of Biological Systems, Scientific Computing Program, Oswaldo Cruz Foundation, Rio de Janeiro, Brazil
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13
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Samocha A, Doh H, Kessenbrock K, Roose JP. Unraveling Heterogeneity in Epithelial Cell Fates of the Mammary Gland and Breast Cancer. Cancers (Basel) 2019; 11:E1423. [PMID: 31554261 PMCID: PMC6826786 DOI: 10.3390/cancers11101423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 09/22/2019] [Accepted: 09/22/2019] [Indexed: 12/14/2022] Open
Abstract
Fluidity in cell fate or heterogeneity in cell identity is an interesting cell biological phenomenon, which at the same time poses a significant obstacle for cancer therapy. The mammary gland seems a relatively straightforward organ with stromal cells and basal- and luminal- epithelial cell types. In reality, the epithelial cell fates are much more complex and heterogeneous, which is the topic of this review. Part of the complexity comes from the dynamic nature of this organ: the primitive epithelial tree undergoes extensively remodeling and expansion during puberty, pregnancy, and lactation and, unlike most other organs, the bulk of mammary gland development occurs late, during puberty. An active cell biological debate has focused on lineage commitment to basal- and luminal- epithelial cell fates by epithelial progenitor and stem cells; processes that are also relevant to cancer biology. In this review, we discuss the current understanding of heterogeneity in mammary gland and recent insights obtained through lineage tracing, signaling assays, and organoid cultures. Lastly, we relate these insights to cancer and ongoing efforts to resolve heterogeneity in breast cancer with single-cell RNAseq approaches.
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Affiliation(s)
- Alexandr Samocha
- Department of Anatomy, University of California, San Francisco, CA 94143, USA.
| | - Hanna Doh
- Department of Anatomy, University of California, San Francisco, CA 94143, USA.
| | - Kai Kessenbrock
- Department of Biological Chemistry, University of California, Irvine, CA 92697, USA.
| | - Jeroen P Roose
- Department of Anatomy, University of California, San Francisco, CA 94143, USA.
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